Prescriptions for GERD cause your stomach to stop producing acids which are required to digest your food. They can also cause some damage to the stomach lining. The most commonly reported side effects included headache, abdominal pain, nausea, and diarrhea. Other side effects of Prilosec (omprazole) for instance includes pains in the stomach, side, or abdomen, possibly radiating to the back, nausea. indigestion, vomiting, stomach pain, diarrhea or loose stools, heartburn, bloody or cloudy urine. chills, general feeling of discomfort or illness, loss of appetite, unusual bleeding or bruising, and others.
Long term, some of these remedies may cause problems with the stomach lining, which may cause the stomach from being able to digest B-12 which may lead to pernicious anemia.

You should ask your doctor about possibly treating your GERD with changes to your diet, or by changing the other prescription medications you are taking which may be causing the GERD.

In some cases it has been possible to identify the foods which are causing the GERD by keeping a food diary and this will help to identify the root of the problem by referring back to the foods eaten just prior to the GERD symptoms.