diff --git a/mkdocs.yml b/mkdocs.yml
index 3d65b4042a52bf3fd298ffbb1ff1f662111532df..884bd16d3adc5332377e6eba125c8c3a1231f354 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -5,8 +5,8 @@ theme:
   name: 'readthedocs'
 
 nav:
-  - Home: index.html
-  - Installation: installation.html
+  - Home: index.md
+  - Installation: installation.md
   - Tutorial 1 Basic local phenotype: tutorials/example1.md
   - Tutorial 2 More complex local phenotype: tutorials/example2.md
   - Tutorial 3 Using a remote git repository: tutorials/example3.md