diff --git a/base-action/test/inline-comment-utils.test.ts b/base-action/test/inline-comment-utils.test.ts
new file mode 100644
index 000000000..43f63dfcb
--- /dev/null
+++ b/base-action/test/inline-comment-utils.test.ts
@@ -0,0 +1,247 @@
+#!/usr/bin/env bun
+
+import { describe, test, expect } from "bun:test";
+import {
+  findExistingRootComment,
+  resolveInReplyTo,
+  type ReviewComment,
+} from "../../src/mcp/inline-comment-utils";
+
+describe("inline-comment-utils", () => {
+  describe("findExistingRootComment", () => {
+    const mockComments: ReviewComment[] = [
+      {
+        id: 100,
+        path: "src/index.ts",
+        line: 42,
+        original_line: 42,
+        in_reply_to_id: null,
+      },
+      {
+        id: 101,
+        path: "src/index.ts",
+        line: 42,
+        original_line: 42,
+        in_reply_to_id: 100, // This is a reply, not a root comment
+      },
+      {
+        id: 102,
+        path: "src/utils.ts",
+        line: 10,
+        original_line: 10,
+        in_reply_to_id: null,
+      },
+      {
+        id: 103,
+        path: "src/index.ts",
+        line: 50,
+        original_line: 55, // original_line differs from current line
+        in_reply_to_id: null,
+      },
+    ];
+
+    test("should find existing root comment on same path and line", () => {
+      const result = findExistingRootComment(mockComments, "src/index.ts", 42);
+      expect(result).toBeDefined();
+      expect(result?.id).toBe(100);
+    });
+
+    test("should not find reply comments (only root comments)", () => {
+      // Comment 101 is on the same line but it's a reply
+      const replyComment = mockComments[1]!;
+      const comments: ReviewComment[] = [replyComment];
+      const result = findExistingRootComment(comments, "src/index.ts", 42);
+      expect(result).toBeUndefined();
+    });
+
+    test("should find comment by original_line when line doesn't match", () => {
+      const result = findExistingRootComment(mockComments, "src/index.ts", 55);
+      expect(result).toBeDefined();
+      expect(result?.id).toBe(103);
+    });
+
+    test("should return undefined when no matching comment exists", () => {
+      const result = findExistingRootComment(mockComments, "src/index.ts", 999);
+      expect(result).toBeUndefined();
+    });
+
+    test("should return undefined when path doesn't match", () => {
+      const result = findExistingRootComment(
+        mockComments,
+        "src/nonexistent.ts",
+        42,
+      );
+      expect(result).toBeUndefined();
+    });
+
+    test("should return undefined when targetLine is undefined", () => {
+      const result = findExistingRootComment(
+        mockComments,
+        "src/index.ts",
+        undefined,
+      );
+      expect(result).toBeUndefined();
+    });
+
+    test("should return undefined when comments array is empty", () => {
+      const result = findExistingRootComment([], "src/index.ts", 42);
+      expect(result).toBeUndefined();
+    });
+  });
+
+  describe("resolveInReplyTo", () => {
+    const mockComments: ReviewComment[] = [
+      {
+        id: 100,
+        path: "src/index.ts",
+        line: 42,
+        original_line: 42,
+        in_reply_to_id: null,
+      },
+      {
+        id: 102,
+        path: "src/utils.ts",
+        line: 10,
+        original_line: 10,
+        in_reply_to_id: null,
+      },
+    ];
+
+    test("should return explicit in_reply_to when provided", () => {
+      const result = resolveInReplyTo(999, mockComments, "src/index.ts", 42);
+      expect(result).toBe(999);
+    });
+
+    test("should auto-detect existing comment when in_reply_to is undefined", () => {
+      const result = resolveInReplyTo(
+        undefined,
+        mockComments,
+        "src/index.ts",
+        42,
+      );
+      expect(result).toBe(100);
+    });
+
+    test("should return undefined when no explicit in_reply_to and no existing comment", () => {
+      const result = resolveInReplyTo(
+        undefined,
+        mockComments,
+        "src/index.ts",
+        999,
+      );
+      expect(result).toBeUndefined();
+    });
+
+    test("should prioritize explicit in_reply_to over auto-detection", () => {
+      // Even though there's an existing comment on line 42, explicit value takes precedence
+      const result = resolveInReplyTo(555, mockComments, "src/index.ts", 42);
+      expect(result).toBe(555);
+    });
+
+    test("should handle empty comments array with undefined in_reply_to", () => {
+      const result = resolveInReplyTo(undefined, [], "src/index.ts", 42);
+      expect(result).toBeUndefined();
+    });
+  });
+
+  describe("auto-deduplication scenarios", () => {
+    test("Scenario: First review creates new comment (no existing comments)", () => {
+      const existingComments: ReviewComment[] = [];
+      const result = resolveInReplyTo(
+        undefined,
+        existingComments,
+        "src/index.ts",
+        42,
+      );
+      // No existing comment, should create new thread
+      expect(result).toBeUndefined();
+    });
+
+    test("Scenario: Second review should reply to first comment (deduplication)", () => {
+      const existingComments: ReviewComment[] = [
+        {
+          id: 100,
+          path: "src/index.ts",
+          line: 42,
+          original_line: 42,
+          in_reply_to_id: null,
+        },
+      ];
+      const result = resolveInReplyTo(
+        undefined,
+        existingComments,
+        "src/index.ts",
+        42,
+      );
+      // Should reply to existing comment instead of creating duplicate
+      expect(result).toBe(100);
+    });
+
+    test("Scenario: Third review should still reply to root comment (not to second reply)", () => {
+      const existingComments: ReviewComment[] = [
+        {
+          id: 100,
+          path: "src/index.ts",
+          line: 42,
+          original_line: 42,
+          in_reply_to_id: null, // Root comment
+        },
+        {
+          id: 101,
+          path: "src/index.ts",
+          line: 42,
+          original_line: 42,
+          in_reply_to_id: 100, // Reply to root
+        },
+      ];
+      const result = resolveInReplyTo(
+        undefined,
+        existingComments,
+        "src/index.ts",
+        42,
+      );
+      // Should reply to root comment (100), not to the reply (101)
+      expect(result).toBe(100);
+    });
+
+    test("Scenario: Different file should not trigger deduplication", () => {
+      const existingComments: ReviewComment[] = [
+        {
+          id: 100,
+          path: "src/index.ts",
+          line: 42,
+          original_line: 42,
+          in_reply_to_id: null,
+        },
+      ];
+      const result = resolveInReplyTo(
+        undefined,
+        existingComments,
+        "src/other.ts", // Different file
+        42,
+      );
+      // Different file, should create new thread
+      expect(result).toBeUndefined();
+    });
+
+    test("Scenario: Different line should not trigger deduplication", () => {
+      const existingComments: ReviewComment[] = [
+        {
+          id: 100,
+          path: "src/index.ts",
+          line: 42,
+          original_line: 42,
+          in_reply_to_id: null,
+        },
+      ];
+      const result = resolveInReplyTo(
+        undefined,
+        existingComments,
+        "src/index.ts",
+        50, // Different line
+      );
+      // Different line, should create new thread
+      expect(result).toBeUndefined();
+    });
+  });
+});
diff --git a/src/create-prompt/index.ts b/src/create-prompt/index.ts
index 66149eac3..3b295407d 100644
--- a/src/create-prompt/index.ts
+++ b/src/create-prompt/index.ts
@@ -555,7 +555,13 @@ ${sanitizeContent(eventData.commentBody)}
 Your request is in <trigger_comment> above${eventData.eventName === "issues" ? ` (or the ${entityType} body for assigned/labeled events)` : ""}.
 
 Decide what's being asked:
-1. **Question or code review** - Answer directly or provide feedback
+1. **Question or code review** - Answer directly or provide feedback${
+    eventData.isPR
+      ? `
+   - For inline comments: Use mcp__github_inline_comment__create_inline_comment to add specific feedback on lines
+   - Duplicate comments are automatically prevented - if a comment exists on a line, yours will be added as a reply`
+      : ""
+  }
 2. **Code change** - Implement the change, commit, and push
 
 Communication:
@@ -735,7 +741,15 @@ ${eventData.eventName === "issue_comment" || eventData.eventName === "pull_reque
         - Look for bugs, security issues, performance problems, and other issues
         - Suggest improvements for readability and maintainability
         - Check for best practices and coding standards
-        - Reference specific code sections with file paths and line numbers${eventData.isPR ? `\n      - AFTER reading files and analyzing code, you MUST call mcp__github_comment__update_claude_comment to post your review` : ""}
+        - Reference specific code sections with file paths and line numbers${
+          eventData.isPR
+            ? `\n      - AFTER reading files and analyzing code, you MUST call mcp__github_comment__update_claude_comment to post your review
+      - INLINE COMMENTS (PR reviews):
+        - You have access to mcp__github_inline_comment__create_inline_comment to add inline comments on specific lines
+        - The tool automatically prevents duplicate comments - if a comment already exists on a line, your comment will be added as a reply to the existing thread
+        - If you see existing comments in the <review_comments> section with comment IDs, you can reference them in your feedback`
+            : ""
+        }
       - Formulate a concise, technical, and helpful response based on the context.
       - Reference specific code with inline formatting or code blocks.
       - Include relevant file paths and line numbers when applicable.${
diff --git a/src/mcp/github-inline-comment-server.ts b/src/mcp/github-inline-comment-server.ts
index 703cda2e0..4d780a724 100644
--- a/src/mcp/github-inline-comment-server.ts
+++ b/src/mcp/github-inline-comment-server.ts
@@ -4,6 +4,7 @@ import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import { z } from "zod";
 import { createOctokit } from "../github/api/client";
 import { sanitizeContent } from "../github/utils/sanitizer";
+import { resolveInReplyTo } from "./inline-comment-utils";
 
 // Get repository and PR information from environment variables
 const REPO_OWNER = process.env.REPO_OWNER;
@@ -67,8 +68,14 @@ server.tool(
       .describe(
         "Specific commit SHA to comment on (defaults to latest commit)",
       ),
+    in_reply_to: z
+      .number()
+      .optional()
+      .describe(
+        "Comment ID to reply to (creates a reply in an existing thread instead of a new thread)",
+      ),
   },
-  async ({ path, body, line, startLine, side, commit_id }) => {
+  async ({ path, body, line, startLine, side, commit_id, in_reply_to }) => {
     try {
       const githubToken = process.env.GITHUB_TOKEN;
 
@@ -124,6 +131,32 @@ server.tool(
         params.line = line;
       }
 
+      // Resolve in_reply_to: use explicit value or auto-detect from existing comments
+      const { data: existingComments } =
+        await octokit.rest.pulls.listReviewComments({
+          owner,
+          repo,
+          pull_number,
+          per_page: 100,
+        });
+
+      const resolvedInReplyTo = resolveInReplyTo(
+        in_reply_to,
+        existingComments,
+        path,
+        line,
+      );
+
+      if (resolvedInReplyTo !== undefined) {
+        params.in_reply_to = resolvedInReplyTo;
+        if (in_reply_to === undefined) {
+          // Auto-deduplication case
+          console.log(
+            `Auto-deduplication: Found existing comment ${resolvedInReplyTo} on ${path}:${line}. Replying to existing thread instead of creating duplicate.`,
+          );
+        }
+      }
+
       const result = await octokit.rest.pulls.createReviewComment(params);
 
       return {
diff --git a/src/mcp/inline-comment-utils.ts b/src/mcp/inline-comment-utils.ts
new file mode 100644
index 000000000..7ead15f45
--- /dev/null
+++ b/src/mcp/inline-comment-utils.ts
@@ -0,0 +1,69 @@
+/**
+ * Utility functions for inline comment handling
+ * Extracted for testability
+ */
+
+export interface ReviewComment {
+  id: number;
+  path: string;
+  line?: number | null;
+  original_line?: number | null;
+  in_reply_to_id?: number | null;
+}
+
+/**
+ * Find an existing root comment on the same line and path
+ * Used for auto-deduplication to reply to existing threads instead of creating duplicates
+ *
+ * @param existingComments - List of existing review comments on the PR
+ * @param targetPath - The file path to check
+ * @param targetLine - The line number to check
+ * @returns The existing root comment if found, otherwise undefined
+ */
+export function findExistingRootComment(
+  existingComments: ReviewComment[],
+  targetPath: string,
+  targetLine: number | undefined,
+): ReviewComment | undefined {
+  if (targetLine === undefined) {
+    return undefined;
+  }
+
+  return existingComments.find(
+    (comment) =>
+      comment.path === targetPath &&
+      (comment.line === targetLine || comment.original_line === targetLine) &&
+      !comment.in_reply_to_id,
+  );
+}
+
+/**
+ * Determine if we should reply to an existing comment
+ * Returns the comment ID to reply to, or undefined to create a new thread
+ *
+ * @param explicitInReplyTo - Explicitly specified comment ID to reply to
+ * @param existingComments - List of existing review comments on the PR
+ * @param targetPath - The file path to check
+ * @param targetLine - The line number to check
+ * @returns Comment ID to reply to, or undefined
+ */
+export function resolveInReplyTo(
+  explicitInReplyTo: number | undefined,
+  existingComments: ReviewComment[],
+  targetPath: string,
+  targetLine: number | undefined,
+): number | undefined {
+  // If explicitly specified, use that
+  if (explicitInReplyTo !== undefined) {
+    return explicitInReplyTo;
+  }
+
+  // Otherwise, try to find an existing comment on the same line
+  const existingComment = findExistingRootComment(
+    existingComments,
+    targetPath,
+    targetLine,
+  );
+
+  return existingComment?.id;
+}