Septic arthritis is caused by microbial infection of the joints. Staphylococcus aureus is the most common cause of this condition. Other bacteria like Neisseria gonorrhoeae, Streptococcus etc can also cause this condition.

 An infection in the body like in the respiratory or urinary tract can lead to septic arthritis because the microorganism can through the blood stream to the joint and cause infection there. A deep wound to the skin in the joint area can also cause microorganism like Staphylococcus to enter and cause infection. Similarly, vascular injection of drugs near the joint area or surgery of the joints can also cause infection. Such incidences are rare though. Neisseria gonorrhoeae is sexually transmitted. It causes gonorrhea which in turn can lead to septic arthritis if the bacteria affected the joints. Besides bacteria, viruses and fungi are also known to cause this condition. Viruses like HIV, hepatitis B virus, rubella virus etc can affect the synovium of the joints and cause infection.

 Similarly mycobacterium and fungi like Mycobacterium tuberculosis, Candida albicans etc are also associated with chronic septic arthritis. A form of infectious arthritis called reactive arthritis also causes pain in the joints although the infection is in another part of the body, not the joint.