I had a negative endoscopy done, but are there any risks or side effects of being on protonix (pantoprazole) long term?

Protonix (pantoprazole) S.E.'s. Protonix (pantoprazole) is a very well tolerated medication, but in the short term it and other proton pump inhibitors can cause a number of dose-dependent side effects including commonly headache and diarrhea. Longer term use carries other consequences (please see my earlier answer on this topic in healthtap) including bone thinning ; risk of infection (like c.Difficile).