Pantoprazole (Protonix) can cause side effects, including nausea, vomiting, diarrhea, headache and abdominal pain. Protonix can also increase the risk of arthralgias, fever, rash and upper respiratory infections. People who have a known hypersensitivity or allergy to pantoprazole, similar medications, or other ingredients in the formulation should not use the medication. Protonix can interact with a number of medications and should used be care when taken with other medications. Bone fractures and hypomagnesemia are risks related to long-term use of pantoprazole. Pantoprazole and alcohol should not be used at the same time. Prior to using Protonix, it is important to discuss possible side effects with one’s medical provider and pharmacist.