Preheat oven to 350 degrees F (175 degrees C).
Melt butter in a medium saucepan over medium heat.Saute onion for 2 minutes.Stir in flour and cook 1 minute, stirring constantly.Stir in milk, salt, mustard and pepper; cook, stirring frequently, until mixture boils and thickens.
Meanwhile,bring a pot of lightly salted water to a boil. Add macaroni and cook for 8 to 10 minutes or until al dente; drain.
To the milk mixture add the Cheddar and American cheeses; stir until cheese melts.Combine macaroni and cheese sauce in a 2 quart baking dish; mix well.
Bake in preheated oven for 30 minutes, or until hot and bubbly.Let cool 10 minutes before serving.
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