Protonix (pantoprazole) is a proton pump inhibitor (PPI) used in the treatment of gastroesophageal reflux disease (GERD) and other stomach conditions. While it is an effective treatment method, some people may experience side effects from taking it, such as gas. Gas is a common side effect of Protonix and is usually due to an increase in the acidity levels in the body. Protonix works by reducing the amount of acid in the stomach, which in turn can lead to the production of more gas. This gas can be uncomfortable, but it is usually short-term and not serious. In addition to gas, other common side effects of Protonix include nausea and diarrhea. If these or any other side effects become severe or persist for more than a few days, it is important to contact your doctor. Your doctor can help you manage any side effects and determine whether or not Protonix is the best treatment option for you.