diff --git a/doc/VectorCode-cli.txt b/doc/VectorCode-cli.txt
index 25589b47..9d675453 100644
--- a/doc/VectorCode-cli.txt
+++ b/doc/VectorCode-cli.txt
@@ -660,17 +660,21 @@ If you used `--include chunk path` parameters, the array will look like this:
             "chunk": "foo",
             "start_line": 1,
             "end_line": 1,
+            "chunk_id": "chunk_id_1"
         },
         {
             "path": "path_to_another_file.py",
             "chunk": "bar",
             "start_line": 1,
             "end_line": 1,
+            "chunk_id": "chunk_id_2"
         }
     ]
 <
 
-Keep in mind that both `start_line` and `end_line` are inclusive.
+Keep in mind that both `start_line` and `end_line` are inclusive. The
+`chunk_id` is a random string that can be used as a unique identifier to
+distinguish between chunks. These are the same IDs used in the database.
 
 
 VECTORCODE VECTORISE
diff --git a/docs/cli.md b/docs/cli.md
index 393ee0a3..8d619b71 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -595,16 +595,20 @@ If you used `--include chunk path` parameters, the array will look like this:
         "chunk": "foo",
         "start_line": 1,
         "end_line": 1,
+        "chunk_id": "chunk_id_1"
     },
     {
         "path": "path_to_another_file.py",
         "chunk": "bar",
         "start_line": 1,
         "end_line": 1,
+        "chunk_id": "chunk_id_2"
     }
 ]
 ```
-Keep in mind that both `start_line` and `end_line` are inclusive.
+Keep in mind that both `start_line` and `end_line` are inclusive. The `chunk_id`
+is a random string that can be used as a unique identifier to distinguish
+between chunks. These are the same IDs used in the database.
 
 #### `vectorcode vectorise`
 The output is in JSON format. It contains a dictionary with the following fields:
diff --git a/lua/vectorcode/integrations/codecompanion/common.lua b/lua/vectorcode/integrations/codecompanion/common.lua
index 4bcc7f1b..987bfcb5 100644
--- a/lua/vectorcode/integrations/codecompanion/common.lua
+++ b/lua/vectorcode/integrations/codecompanion/common.lua
@@ -1,3 +1,5 @@
+---@module "codecompanion"
+
 local job_runner
 local vc_config = require("vectorcode.config")
 local notify_opts = vc_config.notify_opts
@@ -17,8 +19,10 @@ local default_ls_options = {}
 ---@type VectorCode.CodeCompanion.VectoriseToolOpts
 local default_vectorise_options = {}
 
+local TOOL_RESULT_SOURCE = "VectorCodeToolResult"
+
 return {
-  tool_result_source = "VectorCodeToolResult",
+  tool_result_source = TOOL_RESULT_SOURCE,
   ---@param t table|string
   ---@return string
   flatten_table_to_string = function(t)
@@ -122,6 +126,7 @@ return {
     end
     return llm_message
   end,
+
   ---@param use_lsp boolean
   ---@return VectorCode.JobRunner
   initialise_runner = function(use_lsp)
diff --git a/lua/vectorcode/integrations/codecompanion/query_tool.lua b/lua/vectorcode/integrations/codecompanion/query_tool.lua
index 03ac3ff8..a98b0624 100644
--- a/lua/vectorcode/integrations/codecompanion/query_tool.lua
+++ b/lua/vectorcode/integrations/codecompanion/query_tool.lua
@@ -9,6 +9,77 @@ local job_runner = nil
 
 ---@alias QueryToolArgs { project_root:string, count: integer, query: string[] }
 
+---@alias chat_id integer
+---@alias result_id string
+---@type <chat_id: result_id>
+local result_tracker = {}
+
+---@param results VectorCode.QueryResult[]
+---@param chat CodeCompanion.Chat
+---@return VectorCode.QueryResult[]
+local filter_results = function(results, chat)
+  local existing_refs = chat.refs or {}
+
+  existing_refs = vim
+    .iter(existing_refs)
+    :filter(
+      ---@param ref CodeCompanion.Chat.Ref
+      function(ref)
+        return ref.source == cc_common.tool_result_source or ref.path or ref.bufnr
+      end
+    )
+    :map(
+      ---@param ref CodeCompanion.Chat.Ref
+      function(ref)
+        if ref.source == cc_common.tool_result_source then
+          return ref.id
+        elseif ref.path then
+          return ref.path
+        elseif ref.bufnr then
+          return vim.api.nvim_buf_get_name(ref.bufnr)
+        end
+      end
+    )
+    :totable()
+
+  ---@type VectorCode.QueryResult[]
+  local filtered_results = vim
+    .iter(results)
+    :filter(
+      ---@param res VectorCode.QueryResult
+      function(res)
+        -- return true if res should be kept
+        if res.chunk then
+          if res.chunk_id == nil then
+            -- no chunk_id, always include
+            return true
+          end
+          if
+            result_tracker[chat.id] ~= nil and result_tracker[chat.id][res.chunk_id]
+          then
+            return false
+          end
+          return not vim.tbl_contains(existing_refs, res.chunk_id)
+        else
+          if result_tracker[chat.id] ~= nil and result_tracker[chat.id][res.path] then
+            return false
+          end
+          return not vim.tbl_contains(existing_refs, res.path)
+        end
+      end
+    )
+    :totable()
+
+  for _, res in pairs(filtered_results) do
+    if result_tracker[chat.id] == nil then
+      result_tracker[chat.id] = {}
+    end
+    result_tracker[chat.id][res.chunk_id or res.path] = true
+  end
+
+  return filtered_results
+end
+
 ---@param opts VectorCode.CodeCompanion.QueryToolOpts?
 ---@return CodeCompanion.Agent.Tool
 return check_cli_wrap(function(opts)
@@ -148,6 +219,7 @@ You may include multiple keywords in the command.
               description = [[
 Query messages used for the search. They should also contain relevant keywords.
 For example, you should include `parameter`, `arguments` and `return value` for the query `function`.
+If a query returned empty or repeated results, you should avoid using these query keywords, unless the user instructed otherwise.
               ]],
             },
             count = {
@@ -219,6 +291,9 @@ For example, you should include `parameter`, `arguments` and `return value` for
         if opts.max_num > 0 then
           max_result = math.min(opts.max_num or 1, max_result)
         end
+        if opts.no_duplicate then
+          stdout = filter_results(stdout, agent.chat)
+        end
         for i, file in pairs(stdout) do
           if i <= max_result then
             if i == 1 then
@@ -240,14 +315,14 @@ For example, you should include `parameter`, `arguments` and `return value` for
               user_message
             )
             if not opts.chunk_mode then
-              -- skip referencing because there will be multiple chunks with the same path (id).
-              -- TODO: figure out a way to deduplicate.
-              agent.chat.references:add({
+              -- only add to reference if running in full document mode
+              local ref = {
                 source = cc_common.tool_result_source,
                 id = file.path,
                 path = file.path,
                 opts = { visible = false },
-              })
+              }
+              agent.chat.references:add(ref)
             end
           end
         end
diff --git a/lua/vectorcode/types.lua b/lua/vectorcode/types.lua
index 7421a343..779493bf 100644
--- a/lua/vectorcode/types.lua
+++ b/lua/vectorcode/types.lua
@@ -5,6 +5,7 @@
 ---@field chunk string?
 ---@field start_line integer?
 ---@field end_line integer?
+---@field chunk_id string?
 
 ---@class VectorCode.LsResult
 ---@field project-root string
diff --git a/src/vectorcode/subcommands/query/__init__.py b/src/vectorcode/subcommands/query/__init__.py
index 4f4b507a..51c3a550 100644
--- a/src/vectorcode/subcommands/query/__init__.py
+++ b/src/vectorcode/subcommands/query/__init__.py
@@ -114,7 +114,10 @@ async def build_query_results(
                 assert chunk_texts is not None, (
                     "QueryResult does not contain `documents`!"
                 )
-                full_result: dict[str, str | int] = {"chunk": str(chunk_texts[0])}
+                full_result: dict[str, str | int] = {
+                    "chunk": str(chunk_texts[0]),
+                    "chunk_id": identifier,
+                }
                 if meta[0].get("start") is not None and meta[0].get("end") is not None:
                     path = str(meta[0].get("path"))
                     with open(path) as fin:
diff --git a/tests/subcommands/query/test_query.py b/tests/subcommands/query/test_query.py
index a6b17689..4a54de9d 100644
--- a/tests/subcommands/query/test_query.py
+++ b/tests/subcommands/query/test_query.py
@@ -173,6 +173,7 @@ async def test_build_query_results_chunk_mode_success(mock_collection, mock_conf
             "chunk": expected_chunk_content,
             "start_line": start_line,
             "end_line": end_line,
+            "chunk_id": identifier,
         }
 
         assert results[0] == expected_full_result