Woke up with upper stomach pain. i also have a pain in my side wich i believe is muscular.i am concerned about appendicitis but the pain isn't severe?

Appendicitis: Appendicitis pain will almost always go down to the right lower abdomen and also have fever, nausea, vomiting, and lack of appetite. If symptoms worsen see a physician.

Possible other ideas: First advise is that if pain awakened you from sleep, you should see your doctor. The possible answer is gallbladder disease, less likely appendicitis and muscle related pain is a possibility if you recently did any strenuous exercise. Again, best advise is to make an appointment with your primary care doctor.