Mix together flour, flax seed, wheat germ, brown sugar, baking soda, cinnamon, baking powder and salt in a large bowl.
Whisk together milk, eggs and vanilla in a medium bowl. Add to flour mixture, stirring just until moistened. Stir in carrots, apples, walnuts and cranberries.
Fill greased or paper lined muffin cups 3/4 full.
Bake in a preheated 350°F oven for 15 to 20 minutes, or until toothpick inserted in center comes out clean.