Preheat oven to 375°
In a large bowl, combine milk, oil, yogurt, eggs and vanilla. Beat with a whisk until well blended.
In a separate bowl, combine flours, sugar, cocoa powder, baking soda, xanthan gum, baking powder and salt. Stir well to combine.
Pour dry mixture into wet mixture. Stir well to mix. Add chocolate chips, stir again.
Line cupcake tins with paper liners. Fill each about 2/3 or so full.
Bake at 375° F for about 20-25 minutes or until a toothpick inserted in the center of one comes out clean.