diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index acf0dc218da..2c27c7907a9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -26663,7 +26663,9 @@ in
     neuron-version = neuron.version;
   };
 
-  kallisto = callPackage ../applications/science/biology/kallisto { };
+  kallisto = callPackage ../applications/science/biology/kallisto {
+    autoconf = autoconf269;
+  };
 
   kssd = callPackage ../applications/science/biology/kssd { };