Bring 6 cups of water to a rolling boil, add macaroni and cook until just tender. Drain. Meanwhile, melt butter in saucepan over low heat; add flour and stir for about 3 minutes, until frothy. Slowly whisk in milk (which can be pre-heated in the microwave) and stir over medium high until it thickens but does not boil.
Remove from heat and stir in grated cheese, salt and pepper. Stir in macaroni. Pour into baking dish and bake at 350 for 20-30 minutes.