Preheat oven to 350 degrees. Grease muffin tins or line with baking cups.
Mix together flour, flaxseed, wheat germ, brown sugar, baking soda, baking powder, salt and cinnamon in a large bowl. Stir in shredded carrots and apples, chocolate chips or dried fruit and toasted nuts if you are using them.
In a separate, smaller bowl, combine milk, beaten eggs and vanilla. Pour liquid ingredients into dry ingredients. Stir until it is even moistened and distributed, but do not over mix.
Fill muffin cups 3⁄4 full and bake for 15 – 20 minutes or until a knife comes out clean.
Ground flaxseed meal can be found in most grocery stores. Look in the baking or grains section. A widely carried brand is Bob’s Red Mill that comes in a white or yellow bag.