Preheat the oven to 375 degrees F.

Sift the flour and salt and pepper together in a large bowl. Beat the eggs and milk in a medium bowl. Alternately mix the milk mixture into the flour until a smooth dough is formed.

Bring a large pot of salted water to a boil over medium heat Press batter thorough a spaetzle maker into the water. When the spaetzle float to the top of the water, remove them with a slotted spoon to an oven safe dish. After first layer of spaetzle, add a layer of Swiss cheese. Continue layering until all of the spaetzle and cheese have been used.

Bake the spaetzle until the cheese is melted, about 30 minutes.

Melt the butter in a large skillet over low heat. Add the onions and cook until golden brown. Pour over melted spaetzle and serve.

Cook's Note: Spaetzle makers can be found at large department stores.