diff --git a/src/filesystem/__tests__/startup-validation.test.ts b/src/filesystem/__tests__/startup-validation.test.ts
new file mode 100644
index 0000000000..3be283df74
--- /dev/null
+++ b/src/filesystem/__tests__/startup-validation.test.ts
@@ -0,0 +1,100 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { spawn } from 'child_process';
+import * as path from 'path';
+import * as fs from 'fs/promises';
+import * as os from 'os';
+
+const SERVER_PATH = path.join(__dirname, '..', 'dist', 'index.js');
+
+/**
+ * Spawns the filesystem server with given arguments and returns exit info
+ */
+async function spawnServer(args: string[], timeoutMs = 2000): Promise<{ exitCode: number | null; stderr: string }> {
+  return new Promise((resolve) => {
+    const proc = spawn('node', [SERVER_PATH, ...args], {
+      stdio: ['pipe', 'pipe', 'pipe'],
+    });
+
+    let stderr = '';
+    proc.stderr?.on('data', (data) => {
+      stderr += data.toString();
+    });
+
+    const timeout = setTimeout(() => {
+      proc.kill('SIGTERM');
+    }, timeoutMs);
+
+    proc.on('close', (code) => {
+      clearTimeout(timeout);
+      resolve({ exitCode: code, stderr });
+    });
+
+    proc.on('error', (err) => {
+      clearTimeout(timeout);
+      resolve({ exitCode: 1, stderr: err.message });
+    });
+  });
+}
+
+describe('Startup Directory Validation', () => {
+  let testDir: string;
+  let accessibleDir: string;
+  let accessibleDir2: string;
+
+  beforeEach(async () => {
+    testDir = await fs.mkdtemp(path.join(os.tmpdir(), 'fs-startup-test-'));
+    accessibleDir = path.join(testDir, 'accessible');
+    accessibleDir2 = path.join(testDir, 'accessible2');
+    await fs.mkdir(accessibleDir, { recursive: true });
+    await fs.mkdir(accessibleDir2, { recursive: true });
+  });
+
+  afterEach(async () => {
+    await fs.rm(testDir, { recursive: true, force: true });
+  });
+
+  it('should start successfully with all accessible directories', async () => {
+    const result = await spawnServer([accessibleDir, accessibleDir2]);
+    // Server starts and runs (we kill it after timeout, so exit code is null or from SIGTERM)
+    expect(result.stderr).toContain('Secure MCP Filesystem Server running on stdio');
+    expect(result.stderr).not.toContain('Error:');
+  });
+
+  it('should skip inaccessible directory and continue with accessible one', async () => {
+    const nonExistentDir = path.join(testDir, 'non-existent-dir-12345');
+
+    const result = await spawnServer([nonExistentDir, accessibleDir]);
+
+    // Should warn about inaccessible directory
+    expect(result.stderr).toContain('Warning: Cannot access directory');
+    expect(result.stderr).toContain(nonExistentDir);
+
+    // Should still start successfully
+    expect(result.stderr).toContain('Secure MCP Filesystem Server running on stdio');
+  });
+
+  it('should exit with error when ALL directories are inaccessible', async () => {
+    const nonExistent1 = path.join(testDir, 'non-existent-1');
+    const nonExistent2 = path.join(testDir, 'non-existent-2');
+
+    const result = await spawnServer([nonExistent1, nonExistent2]);
+
+    // Should exit with error
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toContain('Error: None of the specified directories are accessible');
+  });
+
+  it('should warn when path is not a directory', async () => {
+    const filePath = path.join(testDir, 'not-a-directory.txt');
+    await fs.writeFile(filePath, 'content');
+
+    const result = await spawnServer([filePath, accessibleDir]);
+
+    // Should warn about non-directory
+    expect(result.stderr).toContain('Warning:');
+    expect(result.stderr).toContain('not a directory');
+
+    // Should still start with the valid directory
+    expect(result.stderr).toContain('Secure MCP Filesystem Server running on stdio');
+  });
+});
diff --git a/src/filesystem/index.ts b/src/filesystem/index.ts
index 48a599fae1..74bf0a9222 100644
--- a/src/filesystem/index.ts
+++ b/src/filesystem/index.ts
@@ -56,19 +56,28 @@ let allowedDirectories = await Promise.all(
   })
 );
 
-// Validate that all directories exist and are accessible
-await Promise.all(allowedDirectories.map(async (dir) => {
+// Filter to only accessible directories, warn about inaccessible ones
+const accessibleDirectories: string[] = [];
+for (const dir of allowedDirectories) {
   try {
     const stats = await fs.stat(dir);
-    if (!stats.isDirectory()) {
-      console.error(`Error: ${dir} is not a directory`);
-      process.exit(1);
+    if (stats.isDirectory()) {
+      accessibleDirectories.push(dir);
+    } else {
+      console.error(`Warning: ${dir} is not a directory, skipping`);
     }
   } catch (error) {
-    console.error(`Error accessing directory ${dir}:`, error);
-    process.exit(1);
+    console.error(`Warning: Cannot access directory ${dir}, skipping`);
   }
-}));
+}
+
+// Exit only if ALL paths are inaccessible (and some were specified)
+if (accessibleDirectories.length === 0 && allowedDirectories.length > 0) {
+  console.error("Error: None of the specified directories are accessible");
+  process.exit(1);
+}
+
+allowedDirectories = accessibleDirectories;
 
 // Initialize the global allowedDirectories in lib.ts
 setAllowedDirectories(allowedDirectories);