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Side effects of glucosamine and chondroitin appeared mild, according to results from the Glucosamine/Chondroitin Arthritis Intervention Trial (GAIT), funded by the National Institutes of Health (NIH). Some people may experience nausea, diarrhea, constipation or heartburn. However, there are no long-term studies on potential adverse effects of glucosamine or chondroitin.

According to the Natural Standard Research Collaboration (NSRC), a number of other side effects may be theoretically possible, or have been associated with (but not proven to be caused by)  the supplements. These include drowsiness, insomnia, headache, skin reactions, abdominal pain, loss of appetite, chest pain, swelling of the eyelids, breathing difficulties.

According to the NSRC, glucosamine and chondroitin should not be given to children under 18 because there is no scientific evidence to recommend their use. Glucosamine is often marketed with MSM (methylsulfonylmethane), which research in children has suggested might have some relationship with autism, according to NSRC.

In addition, studies on animals theoretically suggest the possibility of an increased risk of cataracts with glucosamine and the possible increased risk of bleeding or suppression of bone marrow with chondroitin. Also, since chondroitin can be manufactured from cow cartilage there may be an extremely remote possibility of contamination with the infectious protein (prion) that causes bovine spongiform encephalopathy (BSE, or mad cow disease).

People who take glucosamine and chondroitin are recommended to do so in consultation with their physician. Osteoarthritis and rheumatoid arthritis are chronic conditions, which require regular medical monitoring.