What are bisphosphonates side effects?

Heartburn and. Irritation of the tube that connects the throat to the stomach (esophagus), if you are taking bisphosphonate pills. These side effects can usually be avoided by following instructions for taking your medicine.Headache; constipation, diarrhea, and passing gas; and muscle and joint pain, if you are taking intravenous (IV) bisphosphonate shots.There are more serious side effect but very common.