diff --git a/src/tools/mongodb/read/count.ts b/src/tools/mongodb/read/count.ts
index bd86169b..19782ce1 100644
--- a/src/tools/mongodb/read/count.ts
+++ b/src/tools/mongodb/read/count.ts
@@ -4,17 +4,21 @@ import { ToolArgs, OperationType } from "../../tool.js";
 import { z } from "zod";
 
 export const CountArgs = {
-    query: z
+    filter: z
         .record(z.string(), z.unknown())
         .optional()
         .describe(
-            "The query filter to count documents. Matches the syntax of the filter argument of db.collection.count()"
+            "The query filter to count documents. Matches the syntax of the filter argument of db.collection.countDocuments()"
         ),
+    query: z
+        .record(z.string(), z.unknown())
+        .optional()
+        .describe("Alternative old name for filter. Will be used in db.collection.countDocuments()"),
 };
 
 export class CountTool extends MongoDBToolBase {
     protected name = "count";
-    protected description = "Gets the number of documents in a MongoDB collection";
+    protected description = "Gets the number of documents in a MongoDB collection using countDocuments()";
     protected argsShape = {
         ...DbOperationArgs,
         ...CountArgs,
@@ -22,9 +26,16 @@ export class CountTool extends MongoDBToolBase {
 
     protected operationType: OperationType = "read";
 
-    protected async execute({ database, collection, query }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
+    protected async execute({
+        database,
+        collection,
+        query,
+        filter,
+    }: ToolArgs<typeof this.argsShape>): Promise<CallToolResult> {
         const provider = await this.ensureConnected();
-        const count = await provider.count(database, collection, query);
+        // use either filter or query, since we're using countDocuments, prefer filter
+        const queryFilter = filter || query;
+        const count = await provider.countDocuments(database, collection, queryFilter);
 
         return {
             content: [
diff --git a/tests/integration/tools/mongodb/read/count.test.ts b/tests/integration/tools/mongodb/read/count.test.ts
index 5b288448..1f9e942a 100644
--- a/tests/integration/tools/mongodb/read/count.test.ts
+++ b/tests/integration/tools/mongodb/read/count.test.ts
@@ -8,16 +8,27 @@ import {
 } from "../../../helpers.js";
 
 describeWithMongoDB("count tool", (integration) => {
-    validateToolMetadata(integration, "count", "Gets the number of documents in a MongoDB collection", [
-        {
-            name: "query",
-            description:
-                "The query filter to count documents. Matches the syntax of the filter argument of db.collection.count()",
-            type: "object",
-            required: false,
-        },
-        ...databaseCollectionParameters,
-    ]);
+    validateToolMetadata(
+        integration,
+        "count",
+        "Gets the number of documents in a MongoDB collection using countDocuments()",
+        [
+            {
+                name: "filter",
+                description:
+                    "The query filter to count documents. Matches the syntax of the filter argument of db.collection.countDocuments()",
+                type: "object",
+                required: false,
+            },
+            {
+                name: "query",
+                description: "Alternative old name for filter. Will be used in db.collection.countDocuments()",
+                type: "object",
+                required: false,
+            },
+            ...databaseCollectionParameters,
+        ]
+    );
 
     validateThrowsForInvalidArguments(integration, "count", [
         {},
@@ -79,6 +90,43 @@ describeWithMongoDB("count tool", (integration) => {
                 expect(content).toEqual(`Found ${testCase.expectedCount} documents in the collection "foo"`);
             });
         }
+
+        it("correctly filters documents when using 'filter' parameter", async () => {
+            await integration.connectMcpClient();
+
+            // Using 'filter' parameter - should work correctly after the fix
+            const response = await integration.mcpClient().callTool({
+                name: "count",
+                arguments: {
+                    database: integration.randomDbName(),
+                    collection: "foo",
+                    filter: { age: { $lt: 15 } },
+                },
+            });
+
+            const content = getResponseContent(response.content);
+            expect(content).toEqual('Found 2 documents in the collection "foo"');
+        });
+
+        it("prioritizes filter over query when both are provided", async () => {
+            await integration.connectMcpClient();
+
+            // Using both 'filter' and 'query' parameters
+            const response = await integration.mcpClient().callTool({
+                name: "count",
+                arguments: {
+                    database: integration.randomDbName(),
+                    collection: "foo",
+                    filter: { age: { $lt: 15 } },
+                    query: { age: { $gt: 10 } },
+                },
+            });
+
+            const content = getResponseContent(response.content);
+            // Filter takes precedence over query
+            // Filter is { age: { $lt: 15 } } which matches 2 documents
+            expect(content).toEqual('Found 2 documents in the collection "foo"');
+        });
     });
 
     validateAutoConnectBehavior(integration, "count", () => {