Preheat oven to 350 degrees F (175 degrees C). Grease muffin pan or line with paper muffin liners.
In a large bowl, mix together flour, flax seed, oat bran, brown sugar, baking soda, baking powder, salt and cinnamon. Add the milk, eggs, vanilla and oil; mix until just blended. Stir in the carrots, apples, raisins and nuts. Fill prepared muffin cups 2/3 full with batter.
Bake at 350 F (175 degrees C) for 15 to 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.