Of course! Corn tortillas are actually the more traditional/authentic choice when it comes to enchiladas. If you prefer corn tortillas, they can be used instead of the flour tortillas that the recipe indicates. However, I find that most corn tortillas purchased from the store do not hold up well when making liquid-soaked recipes such as this one. They tend to become soggy and will fall apart with this much enchilada sauce. Thus, I recommended using flour tortilla for the best results. However, that is not to preclude you from using what you prefer, especially if you make your own corn tortillas, which will usually be stronger than those from a store.