Preheat oven to 350°F. Grease cups of a muffin tin.
Mix flour, flax seed, bran, brown sugar, baking soda, baking powder, salt and cinnamon together.
In a separate bowl, combine milk, eggs, vanilla and oil and mix well. Add to dry ingredients. Fold in the carrots, apples, raisins and nuts.
Fill prepared muffin cups two-thirds full with batter. Bake for 15 to 25 minutes.