Preheat the oven to 350 degrees. Line 2 muffin tins with cupcake liners.
In a medium bowl combine the oats, craisins, chocolate chips, walnuts, flax seed, baking soda, salt, and pumpkin spice. Mix well and set aside.
In another medium bowl combine the egg, pumpkin puree, honey, milk, and vanilla. Mix well.
Add the wet ingredient to the dry ingredients and mix until combined.
Spoon the mixture into the prepared muffin cups so that they are 2/3 of the way full.
Bake for 30 minutes or until they cups are cooked through.
Remove from muffin tin and cool on a wire rack.
Store in an air tight container for up to 5 days.