Generally, glucosamine is safe and well-tolerated. There is a risk of allergic reaction. Common side effects include nausea, vomiting, abdominal pain, and diarrhea. Chondroitin has also been shown to be safe. Like glucosamine, chondroitin is also associated with stomach pain, nausea, and diarrhea. It has also been associated with headaches and irregular heartbeat.