diff --git a/.semversioner/next-release/patch-20240911201935470388.json b/.semversioner/next-release/patch-20240911201935470388.json
new file mode 100644
index 0000000000..36b24ff432
--- /dev/null
+++ b/.semversioner/next-release/patch-20240911201935470388.json
@@ -0,0 +1,4 @@
+{
+  "type": "patch",
+  "description": "Calculate new inputs and deleted inputs on update"
+}
diff --git a/graphrag/index/cli.py b/graphrag/index/cli.py
index 869c642ad8..4e99f8e7bf 100644
--- a/graphrag/index/cli.py
+++ b/graphrag/index/cli.py
@@ -13,7 +13,7 @@
 
 from graphrag.config import CacheType, enable_logging_with_config, load_config
 
-from .api import build_index, update_index
+from .api import build_index
 from .graph.extractors.claims.prompts import CLAIM_EXTRACTION_PROMPT
 from .graph.extractors.community_reports.prompts import COMMUNITY_REPORT_PROMPT
 from .graph.extractors.graph.prompts import GRAPH_EXTRACTION_PROMPT
diff --git a/graphrag/index/run/run.py b/graphrag/index/run/run.py
index 55ce71eac6..d54e27c3a9 100644
--- a/graphrag/index/run/run.py
+++ b/graphrag/index/run/run.py
@@ -46,6 +46,7 @@
 from graphrag.index.typing import PipelineRunResult
 
 # Register all verbs
+from graphrag.index.update.files import get_delta_docs
 from graphrag.index.verbs import *  # noqa
 from graphrag.index.workflows import (
     VerbDefinitions,
@@ -111,9 +112,6 @@ async def run_pipeline_with_config(
         else await _create_input(config.input, progress_reporter, root_dir)
     )
 
-    if is_update_run:
-        # TODO: Filter dataset to only include new data (this should be done in the input module)
-        pass
     post_process_steps = input_post_process_steps or _create_postprocess_steps(
         config.input
     )
@@ -123,21 +121,44 @@ async def run_pipeline_with_config(
         msg = "No dataset provided!"
         raise ValueError(msg)
 
-    async for table in run_pipeline(
-        workflows=workflows,
-        dataset=dataset,
-        storage=storage,
-        cache=cache,
-        callbacks=callbacks,
-        input_post_process_steps=post_process_steps,
-        memory_profile=memory_profile,
-        additional_verbs=additional_verbs,
-        additional_workflows=additional_workflows,
-        progress_reporter=progress_reporter,
-        emit=emit,
-        is_resume_run=is_resume_run,
-    ):
-        yield table
+    if is_update_run:
+        delta_dataset = await get_delta_docs(dataset, storage)
+
+        delta_storage = storage.child("delta")
+
+        # Run the pipeline on the new documents
+        async for table in run_pipeline(
+            workflows=workflows,
+            dataset=delta_dataset.new_inputs,
+            storage=delta_storage,
+            cache=cache,
+            callbacks=callbacks,
+            input_post_process_steps=post_process_steps,
+            memory_profile=memory_profile,
+            additional_verbs=additional_verbs,
+            additional_workflows=additional_workflows,
+            progress_reporter=progress_reporter,
+            emit=emit,
+            is_resume_run=False,
+        ):
+            yield table
+
+    else:
+        async for table in run_pipeline(
+            workflows=workflows,
+            dataset=dataset,
+            storage=storage,
+            cache=cache,
+            callbacks=callbacks,
+            input_post_process_steps=post_process_steps,
+            memory_profile=memory_profile,
+            additional_verbs=additional_verbs,
+            additional_workflows=additional_workflows,
+            progress_reporter=progress_reporter,
+            emit=emit,
+            is_resume_run=is_resume_run,
+        ):
+            yield table
 
 
 async def run_pipeline(
diff --git a/graphrag/index/update/__init__.py b/graphrag/index/update/__init__.py
new file mode 100644
index 0000000000..e6966408fb
--- /dev/null
+++ b/graphrag/index/update/__init__.py
@@ -0,0 +1,4 @@
+# Copyright (c) 2024 Microsoft Corporation.
+# Licensed under the MIT License
+
+"""Incremental Indexing main module definition."""
diff --git a/graphrag/index/update/files.py b/graphrag/index/update/files.py
new file mode 100644
index 0000000000..2807fe8104
--- /dev/null
+++ b/graphrag/index/update/files.py
@@ -0,0 +1,61 @@
+# Copyright (c) 2024 Microsoft Corporation.
+# Licensed under the MIT License
+
+"""File management and utils for Incremental Indexing."""
+
+from dataclasses import dataclass
+
+import pandas as pd
+
+from graphrag.index.storage.typing import PipelineStorage
+from graphrag.utils.storage import _load_table_from_storage
+
+
+@dataclass
+class InputDelta:
+    """Dataclass to hold the input delta.
+
+    Attributes
+    ----------
+    new_inputs : pd.DataFrame
+        The new inputs.
+    deleted_inputs : pd.DataFrame
+        The deleted inputs.
+    """
+
+    new_inputs: pd.DataFrame
+    deleted_inputs: pd.DataFrame
+
+
+async def get_delta_docs(
+    input_dataset: pd.DataFrame, storage: PipelineStorage
+) -> InputDelta:
+    """Get the delta between the input dataset and the final documents.
+
+    Parameters
+    ----------
+    input_dataset : pd.DataFrame
+        The input dataset.
+    storage : PipelineStorage
+        The Pipeline storage.
+
+    Returns
+    -------
+    InputDelta
+        The input delta. With new inputs and deleted inputs.
+    """
+    final_docs = await _load_table_from_storage(
+        "create_final_documents.parquet", storage
+    )
+
+    # Select distinct title from final docs and from dataset
+    previous_docs: list[str] = final_docs["title"].unique().tolist()
+    dataset_docs: list[str] = input_dataset["title"].unique().tolist()
+
+    # Get the new documents (using loc to ensure DataFrame)
+    new_docs = input_dataset.loc[~input_dataset["title"].isin(previous_docs)]
+
+    # Get the deleted documents (again using loc to ensure DataFrame)
+    deleted_docs = final_docs.loc[~final_docs["title"].isin(dataset_docs)]
+
+    return InputDelta(new_docs, deleted_docs)