diff --git a/lib/analysis-paths.js b/lib/analysis-paths.js
index 23481b192..e644e6696 100644
--- a/lib/analysis-paths.js
+++ b/lib/analysis-paths.js
@@ -8,19 +8,50 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const core = __importStar(require("@actions/core"));
+function isInterpretedLanguage(language) {
+    return language === 'javascript' || language === 'python';
+}
+// Matches a string containing only characters that are legal to include in paths on windows.
+exports.legalWindowsPathCharactersRegex = /^[^<>:"\|?]*$/;
+// Builds an environment variable suitable for LGTM_INDEX_INCLUDE or LGTM_INDEX_EXCLUDE
+function buildIncludeExcludeEnvVar(paths) {
+    // Ignore anything containing a *
+    paths = paths.filter(p => p.indexOf('*') === -1);
+    // Some characters are illegal in path names in windows
+    if (process.platform === 'win32') {
+        paths = paths.filter(p => p.match(exports.legalWindowsPathCharactersRegex));
+    }
+    return paths.join('\n');
+}
 function includeAndExcludeAnalysisPaths(config, languages) {
+    // The 'LGTM_INDEX_INCLUDE' and 'LGTM_INDEX_EXCLUDE' environment variables
+    // control which files/directories are traversed when scanning.
+    // This allows including files that otherwise would not be scanned, or
+    // excluding and not traversing entire file subtrees.
+    // It does not understand globs or double-globs because that would require it to
+    // traverse the entire file tree to determine which files are matched.
+    // Any paths containing "*" are not included in these.
     if (config.paths.length !== 0) {
-        core.exportVariable('LGTM_INDEX_INCLUDE', config.paths.join('\n'));
+        core.exportVariable('LGTM_INDEX_INCLUDE', buildIncludeExcludeEnvVar(config.paths));
     }
     if (config.pathsIgnore.length !== 0) {
-        core.exportVariable('LGTM_INDEX_EXCLUDE', config.pathsIgnore.join('\n'));
+        core.exportVariable('LGTM_INDEX_EXCLUDE', buildIncludeExcludeEnvVar(config.pathsIgnore));
     }
-    function isInterpretedLanguage(language) {
-        return language === 'javascript' || language === 'python';
+    // The 'LGTM_INDEX_FILTERS' environment variable controls which files are
+    // extracted or ignored. It does not control which directories are traversed.
+    // This does understand the glob and double-glob syntax.
+    const filters = [];
+    filters.push(...config.paths.map(p => 'include:' + p));
+    filters.push(...config.pathsIgnore.map(p => 'exclude:' + p));
+    if (filters.length !== 0) {
+        core.exportVariable('LGTM_INDEX_FILTERS', filters.join('\n'));
     }
-    // Index include/exclude only work in javascript and python
-    // If some other language is detected/configured show a warning
-    if ((config.paths.length !== 0 || config.pathsIgnore.length !== 0) && !languages.every(isInterpretedLanguage)) {
+    // Index include/exclude/filters only work in javascript and python.
+    // If any other languages are detected/configured then show a warning.
+    if ((config.paths.length !== 0 ||
+        config.pathsIgnore.length !== 0 ||
+        filters.length !== 0) &&
+        !languages.every(isInterpretedLanguage)) {
         core.warning('The "paths"/"paths-ignore" fields of the config only have effect for Javascript and Python');
     }
 }
diff --git a/lib/analysis-paths.js.map b/lib/analysis-paths.js.map
index e409927c2..52ece5b9e 100644
--- a/lib/analysis-paths.js.map
+++ b/lib/analysis-paths.js.map
@@ -1 +1 @@
-{"version":3,"file":"analysis-paths.js","sourceRoot":"","sources":["../src/analysis-paths.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AAItC,SAAgB,8BAA8B,CAAC,MAA0B,EAAE,SAAmB;IAC5F,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;QAC7B,IAAI,CAAC,cAAc,CAAC,oBAAoB,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;KACpE;IAED,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;QACnC,IAAI,CAAC,cAAc,CAAC,oBAAoB,EAAE,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;KAC1E;IAED,SAAS,qBAAqB,CAAC,QAAQ;QACrC,OAAO,QAAQ,KAAK,YAAY,IAAI,QAAQ,KAAK,QAAQ,CAAC;IAC5D,CAAC;IAED,2DAA2D;IAC3D,+DAA+D;IAC/D,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,qBAAqB,CAAC,EAAE;QAC7G,IAAI,CAAC,OAAO,CAAC,4FAA4F,CAAC,CAAC;KAC5G;AACH,CAAC;AAlBD,wEAkBC"}
\ No newline at end of file
+{"version":3,"file":"analysis-paths.js","sourceRoot":"","sources":["../src/analysis-paths.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AAItC,SAAS,qBAAqB,CAAC,QAAQ;IACrC,OAAO,QAAQ,KAAK,YAAY,IAAI,QAAQ,KAAK,QAAQ,CAAC;AAC5D,CAAC;AAED,6FAA6F;AAChF,QAAA,+BAA+B,GAAG,eAAe,CAAC;AAE/D,uFAAuF;AACvF,SAAS,yBAAyB,CAAC,KAAe;IAChD,iCAAiC;IACjC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAEjD,uDAAuD;IACvD,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE;QAChC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,uCAA+B,CAAC,CAAC,CAAC;KACrE;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,SAAgB,8BAA8B,CAAC,MAA0B,EAAE,SAAmB;IAC5F,0EAA0E;IAC1E,+DAA+D;IAC/D,sEAAsE;IACtE,qDAAqD;IACrD,gFAAgF;IAChF,sEAAsE;IACtE,sDAAsD;IACtD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;QAC7B,IAAI,CAAC,cAAc,CAAC,oBAAoB,EAAE,yBAAyB,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;KACpF;IACD,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;QACnC,IAAI,CAAC,cAAc,CAAC,oBAAoB,EAAE,yBAAyB,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC;KAC1F;IAED,yEAAyE;IACzE,6EAA6E;IAC7E,wDAAwD;IACxD,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC;IACvD,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC;IAC7D,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;QACxB,IAAI,CAAC,cAAc,CAAC,oBAAoB,EAAE,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;KAC/D;IAED,oEAAoE;IACpE,sEAAsE;IACtE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC;QACxB,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC;QAC/B,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC;QACvB,CAAC,SAAS,CAAC,KAAK,CAAC,qBAAqB,CAAC,EAAE;QAC3C,IAAI,CAAC,OAAO,CAAC,4FAA4F,CAAC,CAAC;KAC5G;AACH,CAAC;AAjCD,wEAiCC"}
\ No newline at end of file
diff --git a/lib/analysis-paths.test.js b/lib/analysis-paths.test.js
index f0f7d1eed..ed564d944 100644
--- a/lib/analysis-paths.test.js
+++ b/lib/analysis-paths.test.js
@@ -20,13 +20,15 @@ ava_1.default("emptyPaths", async (t) => {
     analysisPaths.includeAndExcludeAnalysisPaths(config, []);
     t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
     t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
+    t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
 });
 ava_1.default("nonEmptyPaths", async (t) => {
     let config = new configUtils.Config();
-    config.paths.push('path1', 'path2');
-    config.pathsIgnore.push('path3', 'path4');
+    config.paths.push('path1', 'path2', '**/path3');
+    config.pathsIgnore.push('path4', 'path5', 'path6/**');
     analysisPaths.includeAndExcludeAnalysisPaths(config, []);
     t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
-    t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path3\npath4');
+    t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
+    t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
 });
 //# sourceMappingURL=analysis-paths.test.js.map
\ No newline at end of file
diff --git a/lib/analysis-paths.test.js.map b/lib/analysis-paths.test.js.map
index b010dc038..1116e92c0 100644
--- a/lib/analysis-paths.test.js.map
+++ b/lib/analysis-paths.test.js.map
@@ -1 +1 @@
-{"version":3,"file":"analysis-paths.test.js","sourceRoot":"","sources":["../src/analysis-paths.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AAEvB,gEAAkD;AAClD,4DAA8C;AAC9C,mDAA2C;AAE3C,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC3B,IAAI,MAAM,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;IACtC,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;AACrD,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,eAAe,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC9B,IAAI,MAAM,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;IACtC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IACpC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAC1C,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;IACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;AAC1D,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"analysis-paths.test.js","sourceRoot":"","sources":["../src/analysis-paths.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AAEvB,gEAAkD;AAClD,4DAA8C;AAC9C,mDAA2C;AAE3C,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC3B,IAAI,MAAM,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;IACtC,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;AACrD,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,eAAe,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC9B,IAAI,MAAM,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;IACtC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC,CAAC;IAChD,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC,CAAC;IACtD,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACzD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;IACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;IACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,gGAAgG,CAAC,CAAC;AAC5I,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/config-utils.js b/lib/config-utils.js
index ec534107f..316bc3efc 100644
--- a/lib/config-utils.js
+++ b/lib/config-utils.js
@@ -105,6 +105,52 @@ class Config {
     }
 }
 exports.Config = Config;
+// Regex validating stars in paths or paths-ignore entries.
+// The intention is to only allow ** to appear when immediately
+// preceded and followed by a slash.
+const pathStarsRegex = /.*(?:\*\*[^/].*|\*\*$|[^/]\*\*.*)/;
+// Characters that are supported by filters in workflows, but not by us.
+// See https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
+const filterPatternCharactersRegex = /.*[\?\+\[\]!].*/;
+// Checks that a paths of paths-ignore entry is valid, possibly modifying it
+// to make it valid, or if not possible then throws an error.
+function validateAndSanitisePath(originalPath, propertyName, configFile) {
+    // Take a copy so we don't modify the original path, so we can still construct error messages
+    let path = originalPath;
+    // All paths are relative to the src root, so strip off leading slashes.
+    while (path.charAt(0) === '/') {
+        path = path.substring(1);
+    }
+    // Trailing ** are redundant, so strip them off
+    if (path.endsWith('/**')) {
+        path = path.substring(0, path.length - 2);
+    }
+    // An empty path is not allowed as it's meaningless
+    if (path === '') {
+        throw new Error(getConfigFilePropertyError(configFile, propertyName, '"' + originalPath + '" is not an invalid path. ' +
+            'It is not necessary to include it, and it is not allowed to exclude it.'));
+    }
+    // Check for illegal uses of **
+    if (path.match(pathStarsRegex)) {
+        throw new Error(getConfigFilePropertyError(configFile, propertyName, '"' + originalPath + '" contains an invalid "**" wildcard. ' +
+            'They must be immediately preceeded and followed by a slash as in "/**/", or come at the start or end.'));
+    }
+    // Check for other regex characters that we don't support.
+    // Output a warning so the user knows, but otherwise continue normally.
+    if (path.match(filterPatternCharactersRegex)) {
+        core.warning(getConfigFilePropertyError(configFile, propertyName, '"' + originalPath + '" contains an unsupported character. ' +
+            'The filter pattern characters ?, +, [, ], ! are not supported and will be matched literally.'));
+    }
+    // Ban any uses of backslash for now.
+    // This may not play nicely with project layouts.
+    // This restriction can be lifted later if we determine they are ok.
+    if (path.indexOf('\\') !== -1) {
+        throw new Error(getConfigFilePropertyError(configFile, propertyName, '"' + originalPath + '" contains an "\\" character. These are not allowed in filters. ' +
+            'If running on windows we recommend using "/" instead for path filters.'));
+    }
+    return path;
+}
+exports.validateAndSanitisePath = validateAndSanitisePath;
 function getNameInvalid(configFile) {
     return getConfigFilePropertyError(configFile, NAME_PROPERTY, 'must be a non-empty string');
 }
@@ -216,7 +262,7 @@ async function initConfig() {
             if (typeof path !== "string" || path === '') {
                 throw new Error(getPathsIgnoreInvalid(configFile));
             }
-            config.pathsIgnore.push(path);
+            config.pathsIgnore.push(validateAndSanitisePath(path, PATHS_IGNORE_PROPERTY, configFile));
         });
     }
     if (PATHS_PROPERTY in parsedYAML) {
@@ -227,7 +273,7 @@ async function initConfig() {
             if (typeof path !== "string" || path === '') {
                 throw new Error(getPathsInvalid(configFile));
             }
-            config.paths.push(path);
+            config.paths.push(validateAndSanitisePath(path, PATHS_PROPERTY, configFile));
         });
     }
     return config;
diff --git a/lib/config-utils.js.map b/lib/config-utils.js.map
index 0dbc7fd7a..572e63f66 100644
--- a/lib/config-utils.js.map
+++ b/lib/config-utils.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/config-utils.test.js b/lib/config-utils.test.js
index 36eb718d5..472df1af4 100644
--- a/lib/config-utils.test.js
+++ b/lib/config-utils.test.js
@@ -248,4 +248,41 @@ doInvalidQueryUsesTest("foo@master", c => configUtils.getQueryUsesInvalid(c, "fo
 doInvalidQueryUsesTest("https://github.com/foo/bar@master", c => configUtils.getQueryUsesInvalid(c, "https://github.com/foo/bar@master"));
 doInvalidQueryUsesTest("./foo", c => configUtils.getLocalPathDoesNotExist(c, "foo"));
 doInvalidQueryUsesTest("./..", c => configUtils.getLocalPathOutsideOfRepository(c, ".."));
+const validPaths = [
+    'foo',
+    'foo/',
+    'foo/**',
+    'foo/**/',
+    'foo/**/**',
+    'foo/**/bar/**/baz',
+    '**/',
+    '**/foo',
+    '/foo',
+];
+const invalidPaths = [
+    'a/***/b',
+    'a/**b',
+    'a/b**',
+    '**',
+];
+ava_1.default('path validations', t => {
+    // Dummy values to pass to validateAndSanitisePath
+    const propertyName = 'paths';
+    const configFile = './.github/codeql/config.yml';
+    for (const path of validPaths) {
+        t.truthy(configUtils.validateAndSanitisePath(path, propertyName, configFile));
+    }
+    for (const path of invalidPaths) {
+        t.throws(() => configUtils.validateAndSanitisePath(path, propertyName, configFile));
+    }
+});
+ava_1.default('path sanitisation', t => {
+    // Dummy values to pass to validateAndSanitisePath
+    const propertyName = 'paths';
+    const configFile = './.github/codeql/config.yml';
+    // Valid paths are not modified
+    t.deepEqual(configUtils.validateAndSanitisePath('foo/bar', propertyName, configFile), 'foo/bar');
+    // Trailing stars are stripped
+    t.deepEqual(configUtils.validateAndSanitisePath('foo/**', propertyName, configFile), 'foo/');
+});
 //# sourceMappingURL=config-utils.test.js.map
\ No newline at end of file
diff --git a/lib/config-utils.test.js.map b/lib/config-utils.test.js.map
index ebfe59a14..f5adaa415 100644
--- a/lib/config-utils.test.js.map
+++ b/lib/config-utils.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/src/analysis-paths.test.ts b/src/analysis-paths.test.ts
index 838a0a50a..c98732813 100644
--- a/src/analysis-paths.test.ts
+++ b/src/analysis-paths.test.ts
@@ -11,13 +11,15 @@ test("emptyPaths", async t => {
   analysisPaths.includeAndExcludeAnalysisPaths(config, []);
   t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
   t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
+  t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
 });
 
 test("nonEmptyPaths", async t => {
   let config = new configUtils.Config();
-  config.paths.push('path1', 'path2');
-  config.pathsIgnore.push('path3', 'path4');
+  config.paths.push('path1', 'path2', '**/path3');
+  config.pathsIgnore.push('path4', 'path5', 'path6/**');
   analysisPaths.includeAndExcludeAnalysisPaths(config, []);
   t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
-  t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path3\npath4');
+  t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
+  t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
 });
diff --git a/src/analysis-paths.ts b/src/analysis-paths.ts
index 6a88da05f..57d3d38d1 100644
--- a/src/analysis-paths.ts
+++ b/src/analysis-paths.ts
@@ -2,22 +2,57 @@ import * as core from '@actions/core';
 
 import * as configUtils from './config-utils';
 
+function isInterpretedLanguage(language): boolean {
+  return language === 'javascript' || language === 'python';
+}
+
+// Matches a string containing only characters that are legal to include in paths on windows.
+export const legalWindowsPathCharactersRegex = /^[^<>:"\|?]*$/;
+
+// Builds an environment variable suitable for LGTM_INDEX_INCLUDE or LGTM_INDEX_EXCLUDE
+function buildIncludeExcludeEnvVar(paths: string[]): string {
+  // Ignore anything containing a *
+  paths = paths.filter(p => p.indexOf('*') === -1);
+
+  // Some characters are illegal in path names in windows
+  if (process.platform === 'win32') {
+    paths = paths.filter(p => p.match(legalWindowsPathCharactersRegex));
+  }
+
+  return paths.join('\n');
+}
+
 export function includeAndExcludeAnalysisPaths(config: configUtils.Config, languages: string[]) {
+  // The 'LGTM_INDEX_INCLUDE' and 'LGTM_INDEX_EXCLUDE' environment variables
+  // control which files/directories are traversed when scanning.
+  // This allows including files that otherwise would not be scanned, or
+  // excluding and not traversing entire file subtrees.
+  // It does not understand globs or double-globs because that would require it to
+  // traverse the entire file tree to determine which files are matched.
+  // Any paths containing "*" are not included in these.
   if (config.paths.length !== 0) {
-    core.exportVariable('LGTM_INDEX_INCLUDE', config.paths.join('\n'));
+    core.exportVariable('LGTM_INDEX_INCLUDE', buildIncludeExcludeEnvVar(config.paths));
   }
-
   if (config.pathsIgnore.length !== 0) {
-    core.exportVariable('LGTM_INDEX_EXCLUDE', config.pathsIgnore.join('\n'));
+    core.exportVariable('LGTM_INDEX_EXCLUDE', buildIncludeExcludeEnvVar(config.pathsIgnore));
   }
 
-  function isInterpretedLanguage(language): boolean {
-    return language === 'javascript' || language === 'python';
+  // The 'LGTM_INDEX_FILTERS' environment variable controls which files are
+  // extracted or ignored. It does not control which directories are traversed.
+  // This does understand the glob and double-glob syntax.
+  const filters: string[] = [];
+  filters.push(...config.paths.map(p => 'include:' + p));
+  filters.push(...config.pathsIgnore.map(p => 'exclude:' + p));
+  if (filters.length !== 0) {
+    core.exportVariable('LGTM_INDEX_FILTERS', filters.join('\n'));
   }
 
-  // Index include/exclude only work in javascript and python
-  // If some other language is detected/configured show a warning
-  if ((config.paths.length !== 0 || config.pathsIgnore.length !== 0) && !languages.every(isInterpretedLanguage)) {
+  // Index include/exclude/filters only work in javascript and python.
+  // If any other languages are detected/configured then show a warning.
+  if ((config.paths.length !== 0 ||
+        config.pathsIgnore.length !== 0 ||
+        filters.length !== 0) &&
+      !languages.every(isInterpretedLanguage)) {
     core.warning('The "paths"/"paths-ignore" fields of the config only have effect for Javascript and Python');
   }
 }
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index cb85c38f7..c098d2bed 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -323,3 +323,49 @@ doInvalidQueryUsesTest(
 doInvalidQueryUsesTest(
   "./..",
   c => configUtils.getLocalPathOutsideOfRepository(c, ".."));
+
+const validPaths = [
+  'foo',
+  'foo/',
+  'foo/**',
+  'foo/**/',
+  'foo/**/**',
+  'foo/**/bar/**/baz',
+  '**/',
+  '**/foo',
+  '/foo',
+];
+const invalidPaths = [
+  'a/***/b',
+  'a/**b',
+  'a/b**',
+  '**',
+];
+test('path validations', t => {
+  // Dummy values to pass to validateAndSanitisePath
+  const propertyName = 'paths';
+  const configFile = './.github/codeql/config.yml';
+
+  for (const path of validPaths) {
+    t.truthy(configUtils.validateAndSanitisePath(path, propertyName, configFile));
+  }
+  for (const path of invalidPaths) {
+    t.throws(() => configUtils.validateAndSanitisePath(path, propertyName, configFile));
+  }
+});
+
+test('path sanitisation', t => {
+  // Dummy values to pass to validateAndSanitisePath
+  const propertyName = 'paths';
+  const configFile = './.github/codeql/config.yml';
+
+  // Valid paths are not modified
+  t.deepEqual(
+    configUtils.validateAndSanitisePath('foo/bar', propertyName, configFile),
+    'foo/bar');
+
+  // Trailing stars are stripped
+  t.deepEqual(
+    configUtils.validateAndSanitisePath('foo/**', propertyName, configFile),
+    'foo/');
+});
diff --git a/src/config-utils.ts b/src/config-utils.ts
index cdd39a9bf..5351e2532 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -113,6 +113,77 @@ export class Config {
   }
 }
 
+// Regex validating stars in paths or paths-ignore entries.
+// The intention is to only allow ** to appear when immediately
+// preceded and followed by a slash.
+const pathStarsRegex = /.*(?:\*\*[^/].*|\*\*$|[^/]\*\*.*)/;
+
+// Characters that are supported by filters in workflows, but not by us.
+// See https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#filter-pattern-cheat-sheet
+const filterPatternCharactersRegex = /.*[\?\+\[\]!].*/;
+
+// Checks that a paths of paths-ignore entry is valid, possibly modifying it
+// to make it valid, or if not possible then throws an error.
+export function validateAndSanitisePath(
+  originalPath: string,
+  propertyName: string,
+  configFile: string): string {
+
+  // Take a copy so we don't modify the original path, so we can still construct error messages
+  let path = originalPath;
+
+  // All paths are relative to the src root, so strip off leading slashes.
+  while (path.charAt(0) === '/') {
+    path = path.substring(1);
+  }
+
+  // Trailing ** are redundant, so strip them off
+  if (path.endsWith('/**')) {
+    path = path.substring(0, path.length - 2);
+  }
+
+  // An empty path is not allowed as it's meaningless
+  if (path === '') {
+    throw new Error(getConfigFilePropertyError(
+      configFile,
+      propertyName,
+      '"' + originalPath + '" is not an invalid path. ' +
+        'It is not necessary to include it, and it is not allowed to exclude it.'));
+  }
+
+  // Check for illegal uses of **
+  if (path.match(pathStarsRegex)) {
+    throw new Error(getConfigFilePropertyError(
+      configFile,
+      propertyName,
+      '"' + originalPath + '" contains an invalid "**" wildcard. ' +
+        'They must be immediately preceeded and followed by a slash as in "/**/", or come at the start or end.'));
+  }
+
+  // Check for other regex characters that we don't support.
+  // Output a warning so the user knows, but otherwise continue normally.
+  if (path.match(filterPatternCharactersRegex)) {
+    core.warning(getConfigFilePropertyError(
+      configFile,
+      propertyName,
+      '"' + originalPath + '" contains an unsupported character. ' +
+        'The filter pattern characters ?, +, [, ], ! are not supported and will be matched literally.'));
+  }
+
+  // Ban any uses of backslash for now.
+  // This may not play nicely with project layouts.
+  // This restriction can be lifted later if we determine they are ok.
+  if (path.indexOf('\\') !== -1) {
+    throw new Error(getConfigFilePropertyError(
+      configFile,
+      propertyName,
+      '"' + originalPath + '" contains an "\\" character. These are not allowed in filters. ' +
+        'If running on windows we recommend using "/" instead for path filters.'));
+  }
+
+  return path;
+}
+
 export function getNameInvalid(configFile: string): string {
   return getConfigFilePropertyError(configFile, NAME_PROPERTY, 'must be a non-empty string');
 }
@@ -243,7 +314,7 @@ async function initConfig(): Promise<Config> {
       if (typeof path !== "string" || path === '') {
         throw new Error(getPathsIgnoreInvalid(configFile));
       }
-      config.pathsIgnore.push(path);
+      config.pathsIgnore.push(validateAndSanitisePath(path, PATHS_IGNORE_PROPERTY, configFile));
     });
   }
 
@@ -255,7 +326,7 @@ async function initConfig(): Promise<Config> {
       if (typeof path !== "string" || path === '') {
         throw new Error(getPathsInvalid(configFile));
       }
-      config.paths.push(path);
+      config.paths.push(validateAndSanitisePath(path, PATHS_PROPERTY, configFile));
     });
   }