diff --git a/.changeset/null-prototype-mcp-registries.md b/.changeset/null-prototype-mcp-registries.md
new file mode 100644
index 0000000000..26c5899b28
--- /dev/null
+++ b/.changeset/null-prototype-mcp-registries.md
@@ -0,0 +1,5 @@
+---
+'@modelcontextprotocol/server': patch
+---
+
+McpServer tool/prompt/resource registries now use null-prototype objects so names inherited from `Object.prototype` (`constructor`, `toString`, `__proto__`, …) can be registered, listed, and called like any other name.
diff --git a/packages/server/src/server/mcp.ts b/packages/server/src/server/mcp.ts
index bfb3b798b0..b5751d9c59 100644
--- a/packages/server/src/server/mcp.ts
+++ b/packages/server/src/server/mcp.ts
@@ -117,14 +117,16 @@ export class McpServer {
 
     private readonly _maxToolInputElements: number | undefined;
 
-    private _registeredResources: { [uri: string]: RegisteredResource } = {};
+    // Null-prototype maps so names inherited from Object.prototype
+    // (constructor, toString, __proto__, …) are not treated as already registered.
+    private _registeredResources: { [uri: string]: RegisteredResource } = Object.create(null);
     private _registeredResourceTemplates: {
         [name: string]: RegisteredResourceTemplate;
-    } = {};
-    private _registeredTools: { [name: string]: RegisteredTool } = {};
-    private _registeredPrompts: { [name: string]: RegisteredPrompt } = {};
+    } = Object.create(null);
+    private _registeredTools: { [name: string]: RegisteredTool } = Object.create(null);
+    private _registeredPrompts: { [name: string]: RegisteredPrompt } = Object.create(null);
     /** Per-tool JSON-converted `inputSchema`, filled on first use by `toolInputSchemaJson()`. */
-    private _toolInputSchemaJson: { [name: string]: Record<string, unknown> } = {};
+    private _toolInputSchemaJson: { [name: string]: Record<string, unknown> } = Object.create(null);
 
     /**
      * The JSON-serialized `inputSchema` of a registered tool, or `undefined`
diff --git a/packages/server/test/server/registerPrototypeNames.test.ts b/packages/server/test/server/registerPrototypeNames.test.ts
new file mode 100644
index 0000000000..8cc23483f0
--- /dev/null
+++ b/packages/server/test/server/registerPrototypeNames.test.ts
@@ -0,0 +1,92 @@
+import type { JSONRPCMessage } from '@modelcontextprotocol/core-internal';
+import { InMemoryTransport, LATEST_PROTOCOL_VERSION } from '@modelcontextprotocol/core-internal';
+import { describe, expect, it, vi } from 'vitest';
+
+import { McpServer, ResourceTemplate } from '../../src/index.js';
+
+/**
+ * Names that are inherited as own properties of Object.prototype. Indexing a
+ * plain `{}` registry by these names finds the inherited member, so
+ * registerTool/Prompt/Resource treat an empty server as already registered.
+ */
+const PROTOTYPE_NAMES = ['constructor', 'toString', '__proto__', 'hasOwnProperty', 'valueOf'] as const;
+
+describe('McpServer registries ignore Object.prototype names', () => {
+    it.each(PROTOTYPE_NAMES)('registerTool accepts %s on an empty server', name => {
+        const server = new McpServer({ name: 'r', version: '0' });
+        expect(() =>
+            server.registerTool(name, { description: 'x' }, async () => ({ content: [{ type: 'text', text: name }] }))
+        ).not.toThrow();
+    });
+
+    it.each(PROTOTYPE_NAMES)('registerPrompt accepts %s on an empty server', name => {
+        const server = new McpServer({ name: 'r', version: '0' });
+        expect(() =>
+            server.registerPrompt(name, { description: 'x' }, async () => ({
+                messages: [{ role: 'user' as const, content: { type: 'text' as const, text: name } }]
+            }))
+        ).not.toThrow();
+    });
+
+    it.each(PROTOTYPE_NAMES)('registerResource template accepts %s on an empty server', name => {
+        const server = new McpServer({ name: 'r', version: '0' });
+        const template = new ResourceTemplate('proto://{id}', { list: undefined });
+        expect(() =>
+            server.registerResource(name, template, { description: 'x' }, async uri => ({
+                contents: [{ uri: uri.href, text: name }]
+            }))
+        ).not.toThrow();
+    });
+
+    it('lists and calls a tool whose name is inherited from Object.prototype', async () => {
+        const server = new McpServer({ name: 'r', version: '0' });
+        server.registerTool('constructor', { description: 'x' }, async () => ({
+            content: [{ type: 'text', text: 'from-constructor' }]
+        }));
+
+        const [client, srv] = InMemoryTransport.createLinkedPair();
+        await server.connect(srv);
+        await client.start();
+
+        const responses: JSONRPCMessage[] = [];
+        client.onmessage = m => responses.push(m);
+
+        await client.send({
+            jsonrpc: '2.0',
+            id: 1,
+            method: 'initialize',
+            params: {
+                protocolVersion: LATEST_PROTOCOL_VERSION,
+                capabilities: {},
+                clientInfo: { name: 'c', version: '1.0.0' }
+            }
+        } as JSONRPCMessage);
+        await client.send({ jsonrpc: '2.0', method: 'notifications/initialized' } as JSONRPCMessage);
+        await client.send({ jsonrpc: '2.0', id: 2, method: 'tools/list' } as JSONRPCMessage);
+        await client.send({
+            jsonrpc: '2.0',
+            id: 3,
+            method: 'tools/call',
+            params: { name: 'constructor', arguments: {} }
+        } as JSONRPCMessage);
+
+        await vi.waitFor(() => expect(responses.some(r => 'id' in r && r.id === 3)).toBe(true));
+        const listed = responses.find(r => 'id' in r && r.id === 2) as { result?: { tools: Array<{ name: string }> } };
+        expect(listed.result?.tools.map(t => t.name)).toContain('constructor');
+
+        const called = responses.find(r => 'id' in r && r.id === 3) as {
+            result?: { content: Array<{ type: string; text?: string }> };
+            error?: unknown;
+        };
+        expect(called.error).toBeUndefined();
+        expect(called.result?.content?.[0]?.text).toBe('from-constructor');
+
+        await server.close();
+    });
+
+    it('still rejects a true duplicate registration', () => {
+        const server = new McpServer({ name: 'r', version: '0' });
+        server.registerTool('constructor', { description: 'x' }, async () => ({ content: [] }));
+        expect(() => server.registerTool('constructor', { description: 'y' }, async () => ({ content: [] }))).toThrow(/already registered/);
+    });
+});