diff --git a/src/core/file/fileSearch.ts b/src/core/file/fileSearch.ts
index 8e3e885e4..e632d8a4a 100644
--- a/src/core/file/fileSearch.ts
+++ b/src/core/file/fileSearch.ts
@@ -57,6 +57,17 @@ const isGitWorktreeRef = async (gitPath: string): Promise<boolean> => {
   }
 };
 
+/**
+ * Escapes special characters in glob patterns to handle paths with parentheses.
+ * Example: "src/(categories)" -> "src/\\(categories\\)"
+ */
+export const escapeGlobPattern = (pattern: string): string => {
+  // First escape backslashes
+  const escapedBackslashes = pattern.replace(/\\/g, '\\\\');
+  // Then escape special characters
+  return escapedBackslashes.replace(/[()[\]{}]/g, '\\$&');
+};
+
 // Get all file paths considering the config
 export const searchFiles = async (rootDir: string, config: RepomixConfigMerged): Promise<FileSearchResult> => {
   // First check directory permissions
@@ -69,7 +80,8 @@ export const searchFiles = async (rootDir: string, config: RepomixConfigMerged):
     throw new Error(`Cannot access directory ${rootDir}: ${permissionCheck.error?.message}`);
   }
 
-  const includePatterns = config.include.length > 0 ? config.include : ['**/*'];
+  const includePatterns =
+    config.include.length > 0 ? config.include.map((pattern) => escapeGlobPattern(pattern)) : ['**/*'];
 
   try {
     const [ignorePatterns, ignoreFilePatterns] = await Promise.all([
diff --git a/tests/core/file/fileSearch.test.ts b/tests/core/file/fileSearch.test.ts
index ab89b7142..35ff061b2 100644
--- a/tests/core/file/fileSearch.test.ts
+++ b/tests/core/file/fileSearch.test.ts
@@ -6,6 +6,7 @@ import { globby } from 'globby';
 import { minimatch } from 'minimatch';
 import { beforeEach, describe, expect, test, vi } from 'vitest';
 import {
+  escapeGlobPattern,
   getIgnoreFilePatterns,
   getIgnorePatterns,
   parseIgnoreContent,
@@ -342,4 +343,50 @@ node_modules
       expect(result.filePaths).toEqual(['file1.js', 'file2.js']);
     });
   });
+
+  describe('escapeGlobPattern', () => {
+    test('should escape parentheses in pattern', () => {
+      const pattern = 'src/(categories)/**/*.ts';
+      expect(escapeGlobPattern(pattern)).toBe('src/\\(categories\\)/**/*.ts');
+    });
+
+    test('should escape multiple types of brackets', () => {
+      const pattern = 'src/(auth)/[id]/{slug}/**/*.ts';
+      expect(escapeGlobPattern(pattern)).toBe('src/\\(auth\\)/\\[id\\]/\\{slug\\}/**/*.ts');
+    });
+
+    test('should handle nested brackets', () => {
+      const pattern = 'src/(auth)/([id])/**/*.ts';
+      expect(escapeGlobPattern(pattern)).toBe('src/\\(auth\\)/\\(\\[id\\]\\)/**/*.ts');
+    });
+
+    test('should handle empty string', () => {
+      expect(escapeGlobPattern('')).toBe('');
+    });
+
+    test('should not modify patterns without special characters', () => {
+      const pattern = 'src/components/**/*.ts';
+      expect(escapeGlobPattern(pattern)).toBe(pattern);
+    });
+
+    test('should handle multiple occurrences of the same bracket type', () => {
+      const pattern = 'src/(auth)/(settings)/**/*.ts';
+      expect(escapeGlobPattern(pattern)).toBe('src/\\(auth\\)/\\(settings\\)/**/*.ts');
+    });
+  });
+
+  test('should escape backslashes in pattern', () => {
+    const pattern = 'src\\temp\\(categories)';
+    expect(escapeGlobPattern(pattern)).toBe('src\\\\temp\\\\\\(categories\\)');
+  });
+
+  test('should handle patterns with already escaped special characters', () => {
+    const pattern = 'src\\\\(categories)';
+    expect(escapeGlobPattern(pattern)).toBe('src\\\\\\\\\\(categories\\)');
+  });
+
+  test('should handle patterns with mixed backslashes and special characters', () => {
+    const pattern = 'src\\temp\\[id]\\{slug}';
+    expect(escapeGlobPattern(pattern)).toBe('src\\\\temp\\\\\\[id\\]\\\\\\{slug\\}');
+  });
 });