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Hi Susan Schecter,
Proton Pump Inhibitors like Nexium and Prilosec have been determined to be safe for long term use and do have diarrhea listed as a potential side effect. There is some controversy however about proton pump inhibitors contributing to bone issues, specifically hip problems. You can read more about that in this share post by Dr Todd Esiner. You can also read a post by Dr Eisner about long term use here, question 5.
I hope this helps. Stay in touch and let us know how you are doing!Vicki M