Preheat waffle iron. In a large bowl, whisk the all purpose and whole wheat flours together with the flax seeds, baking powder, salt and sugar.
In a separate bowl, whisk together the lightly beaten eggs, melted butter and milk. Pour over the flour mixture and stir gently with a wooden spoon until just combined. Fold in blueberries.
Brush waffle iron with melted butter, and spoon waffle batter into the centre (about 1/3 cup batter per waffle, or according to the manufacturer’s directions). Bake until golden brown. Serve immediately or keep warm in a 200ºF oven.