Preheat oven to 350. Brown beef and onion. Drain the fat and sprinkle with the salt and pepper.
Place half the chilies in a 9 x 13 baking dish or a lasagna pan. Sprinkle with cheese and top with meat mixture. Place the rest of the chilies over the meat.
Combine the remaining ingredients, beating until smooth. Pour over the meat and chilies mixture. Bake at 350 for 45 to 50 minutes or until a knife inserted off center comes out clean. Let cool 5 minutes.