Sn explain that the joint pain can affect one or more joints. The joint pain can be caused by many types of injuries or conditions. It may be linked to arthritis, bursitis, and muscle pain. No matter what causes it, this can be very bothersome. Some things that can cause joint pain are: Autoimmune diseases such as rheumatoid arthritis and lupus Bursitis Chondromalacia patellae Crystals in the joint: Gout ( especially found in the big toe ) and Calcium pyrophosphate deposition (CPPD ) ( pseudo gout ) Infections caused by a virusInjury, such as a fracture Osteoarthritis Osteomyelitis ( bone infection ), Septic arthritis ( joint infection ) Tendinitis Unusual exertion or overuse, including strains or sprains.