diff --git a/pkgs/development/python-modules/pyvcf/default.nix b/pkgs/development/python-modules/pyvcf/default.nix
deleted file mode 100644
index 1efcdd4d2242..000000000000
--- a/pkgs/development/python-modules/pyvcf/default.nix
+++ /dev/null
@@ -1,33 +0,0 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, pytest
-}:
-
-buildPythonPackage rec {
-  pname = "PyVCF";
-  version = "0.6.8";
-
-  src = fetchFromGitHub {
-    owner = "jamescasbon";
-    repo = "PyVCF";
-    rev = "476169cd457ba0caa6b998b301a4d91e975251d9";
-    sha256 = "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p";
-  };
-
-  nativeCheckInputs = [ pytest ];
-
-  meta = with lib; {
-    homepage = "https://pyvcf.readthedocs.io/en/latest/index.html";
-    description = "A VCF (Variant Call Format) Parser for Python, supporting version 4.0 and 4.1";
-    license = licenses.bsd3;
-    maintainers = with maintainers; [ scalavision ];
-    longDescription = ''
-      The intent of this module is to mimic the csv module in the Python stdlib,
-      as opposed to more flexible serialization formats like JSON or YAML.
-      vcf will attempt to parse the content of each record based on the data
-      types specified in the meta-information lines
-    '';
-    broken = true; # uses the 2to3 feature, that got removed in setuptools 0.58
-  };
-}
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index bc530590cb13..53b9ccd520b4 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -251,6 +251,7 @@ mapAliases ({
   pytorchWithCuda = torchWithCuda; # added 2022-09-30
   pytorchWithoutCuda = torchWithoutCuda; # added 2022-09-30
   pytwitchapi = twitchapi; # added 2022-03-07
+  pyvcf = throw "pyvcf has been removed, it was using setuptools 2to3 translation feature, which has been removed in setuptools 58"; # added 2023-05-19
   PyVirtualDisplay = pyvirtualdisplay; # added 2023-02-19
   qasm2image = throw "qasm2image is no longer maintained (since November 2018), and is not compatible with the latest pythonPackages.qiskit versions."; # added 2020-12-09
   Quandl = quandl; # added 2023-02-19
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 68153a8f7647..6d9722e67e3b 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10043,8 +10043,6 @@ self: super: with self; {
 
   pyvcd = callPackage ../development/python-modules/pyvcd { };
 
-  pyvcf = callPackage ../development/python-modules/pyvcf { };
-
   pyvera = callPackage ../development/python-modules/pyvera { };
 
   pyverilog = callPackage ../development/python-modules/pyverilog { };