Preheat the oven to 350°F.
Lightly oil or coat 12 muffin cups with nonstick cooking spray and set aside.
Whisk together the all-purpose flour, whole wheat flour, wheat germ, baking powder, and salt in a large bowl.
Combine the bananas, eggs, sugar, oil, milk, and vanilla in a medium bowl and stir until well blended. Pour the liquid ingredients over the dry ingredients and stir until just moistened. Stir in the chocolate chips.
Spoon the batter into the prepared muffin cups. Bake about 20 minutes, or until the muffins are light golden and a toothpick inserted in the center comes out clean.
Transfer the pan to a wire rack and cool for 5 minutes. Remove the muffins and cool an additional 5 minutes before serving. To make 24 mini muffins, bake about 14 minutes.