Preheat the oven to 375 degrees. Butter a 1 1/2 quart souffle dish. In a heavy-bottomed saucepan, bring the milk to a boil, being careful not to allow it to scorch or boil over. Remove from the heat and reserve. In a second saucepan, melt the butter over low heat. Add the flour, stirring with a wooden spoon, until completely combined. Pour 1/3 of the milk into the butter mixture and, using a wire whisk, incorporate it completely before adding the remaining milk. When all of the milk has been added, continue cooking over low heat for 5 minutes.
Add the cheese to the hot milk mixture, stirring carefully. Do not let the mixture boil or the cheese will separate. Stir in the jalapeno, salt and pepper and remove from heat.
Let the liquid cool for 5 minutes, add several tablespoons of liquid to the egg yolks and stir together. Then add the yolks to the cheese and milk mixture slowly, stirring with a wooden spoon. Transfer the mixture to a mixing bowl and allow to cool completely before finishing the souffle. In a mixing bowl, whisk the egg whites to stiff peaks. Fold 1/3 of the beaten whites into the cheese mixture and then carefully fold in the remaining whites, being careful not to deflate the whites. Pour the souffle mixture into the souffle dish and bake for 45 minutes. Serve immediately.