Preheat oven to 375 degrees and grease muffin pans.
In a large bowl, combine the flours, oats, brown sugar, cinnamon, baking soda, baking powder and salt, stir.
Add the shredded apples, carrots, walnuts and raisins and stir until coated.
In a small bowl, stir together eggs, milk and oil. Pour into the flour mixture and stir just until everything is moistened. Fill muffin pans about ¾ full.
Bake in preheated oven for 18 to 20 minutes for regular muffins or 12 to 15 minutes for mini muffins.
Remove from oven and place on wire racks to cool slightly.