Preheat oven to 450 F.
Chop chives and combine with flour, salt and thyme. In a separate bowl, whisk eggs and milk. Gradually add the milk mixture to the flour mixture until the batter is smooth. Refrigerate up to 1 hour, if desired.
Butter the bottoms of a muffin pan and then fill each one halfway with batter. Bake in the oven for 15 to 18 minutes or until puffed and golden.