diff --git a/pkgs/development/python-modules/anndata/default.nix b/pkgs/development/python-modules/anndata/default.nix
new file mode 100644
index 000000000000..4e79d8b013d8
--- /dev/null
+++ b/pkgs/development/python-modules/anndata/default.nix
@@ -0,0 +1,158 @@
+{
+  array-api-compat,
+  awkward,
+  boltons,
+  buildPythonPackage,
+  dask,
+  distributed,
+  fetchFromGitHub,
+  filelock,
+  h5py,
+  hatch-vcs,
+  hatchling,
+  joblib,
+  lib,
+  natsort,
+  numba,
+  numpy,
+  openpyxl,
+  packaging,
+  pandas,
+  pyarrow,
+  pytest-mock,
+  pytest-xdist,
+  pytestCheckHook,
+  pythonOlder,
+  scikit-learn,
+  scipy,
+  stdenv,
+  typing-extensions,
+  zarr,
+}:
+
+buildPythonPackage rec {
+  pname = "anndata";
+  version = "0.11.4";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "scverse";
+    repo = "anndata";
+    tag = version;
+    hash = "sha256-9RDR0veZ8n2sq0kUbAkS2nP57u47cQxmubzuWWYBKBY=";
+  };
+
+  build-system = [
+    hatch-vcs
+    hatchling
+  ];
+
+  dependencies = [
+    array-api-compat
+    h5py
+    natsort
+    numpy
+    pandas
+    scipy
+  ];
+
+  nativeCheckInputs = [
+    awkward
+    boltons
+    dask
+    distributed
+    filelock
+    joblib
+    numba
+    openpyxl
+    pyarrow
+    pytest-mock
+    pytest-xdist
+    pytestCheckHook
+    scikit-learn
+    zarr
+  ];
+
+  # Optionally disable pytest-xdist to make it easier to debug the test suite.
+  # Test suite takes ~5 minutes without pytest-xdist. Note that some tests will
+  # fail when running without pytest-xdist ("worker_id not found").
+  # pytestFlagsArray = [ "-o" "addopts=" ];
+
+  disabledTestPaths = [
+    # Tests that require scanpy, creating a circular dependency chain
+    "src/anndata/_core/anndata.py"
+    "src/anndata/_core/merge.py"
+    "src/anndata/_core/sparse_dataset.py"
+    "src/anndata/_io/specs/registry.py"
+    "src/anndata/_io/utils.py"
+    "src/anndata/_warnings.py"
+    "src/anndata/experimental/merge.py"
+    "src/anndata/experimental/multi_files/_anncollection.py"
+    "src/anndata/utils.py"
+  ];
+
+  disabledTests =
+    [
+      # doctests that require scanpy, creating a circular dependency chain. These
+      # do not work in disabledTestPaths for some reason.
+      "anndata._core.anndata.AnnData.concatenate"
+      "anndata._core.anndata.AnnData.obs_names_make_unique"
+      "anndata._core.anndata.AnnData.var_names_make_unique"
+      "anndata._core.merge.concat"
+      "anndata._core.merge.gen_reindexer"
+      "anndata._core.sparse_dataset.sparse_dataset"
+      "anndata._io.specs.registry.read_elem_as_dask"
+      "anndata._io.utils.report_read_key_on_error"
+      "anndata._io.utils.report_write_key_on_error"
+      "anndata._warnings.ImplicitModificationWarning"
+      "anndata.experimental.merge.concat_on_disk"
+      "anndata.experimental.multi_files._anncollection.AnnCollection"
+      "anndata.utils.make_index_unique"
+      "ci.scripts.min-deps.min_dep"
+      "concatenation.rst"
+
+      # Tests that require cupy and GPU access. Introducing cupy as a dependency
+      # would make this package unfree and GPU access is not possible within the
+      # nix build environment anyhow.
+      "test_adata_raw_gpu"
+      "test_as_cupy_dask"
+      "test_as_dask_functions"
+      "test_concat_different_types_dask"
+      "test_concat_on_var_outer_join"
+      "test_concatenate_layers_misaligned"
+      "test_concatenate_layers_outer"
+      "test_concatenate_layers"
+      "test_concatenate_roundtrip"
+      "test_dask_to_memory_unbacked"
+      "test_ellipsis_index"
+      "test_error_on_mixed_device"
+      "test_gpu"
+      "test_io_spec_cupy"
+      "test_modify_view_component"
+      "test_nan_merge"
+      "test_pairwise_concat"
+      "test_raw_gpu"
+      "test_set_scalar_subset_X"
+      "test_transposed_concat"
+      "test_view_different_type_indices"
+      "test_view_of_view"
+
+      # Tests that are seemingly broken. See https://github.com/scverse/anndata/issues/2017.
+      "test_concat_dask_sparse_matches_memory"
+    ]
+    ++ lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [
+      # RuntimeError: Cluster failed to start: [Errno 1] Operation not permitted
+      "test_dask_distributed_write"
+      "test_read_lazy_h5_cluster"
+    ];
+
+  pythonImportsCheck = [ "anndata" ];
+
+  meta = {
+    changelog = "https://github.com/scverse/anndata/blob/main/docs/release-notes/${version}.md";
+    description = "Python package for handling annotated data matrices in memory and on disk";
+    homepage = "https://anndata.readthedocs.io/";
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ samuela ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 8bf8b075bc19..56ce5f4d779d 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -681,6 +681,8 @@ self: super: with self; {
 
   anitopy = callPackage ../development/python-modules/anitopy { };
 
+  anndata = callPackage ../development/python-modules/anndata { };
+
   annexremote = callPackage ../development/python-modules/annexremote { };
 
   annotated-types = callPackage ../development/python-modules/annotated-types { };