At present, the mechanism (pathophysiology) behind this infection is unknown but researchers at the NIMH are pursuing a theory that the mechanism is similar to that of rheumatic fever, an autoimmune disorder triggered by a reaction to the antibodies to streptococcal infections, in which these antibodies attack similar regions of the brain that are affected in some neuropsychiatric conditions. In every bacterial infection, the body produces antibodies against the invading bacteria, and the antibodies help eliminate the bacteria from the body. However in rheumatic fever, the antibodies mistakenly recognize and "attack" the heart valves, joints, and/or certain parts of the brain. This phenomenon is called "molecular mimicry", which means that proteins on the cell wall of the strep. bacteria are similar in some way to the proteins of the heart valve, joints, or brain. Because the antibodies set off an immune reaction which damages those tissues, the child with rheumatic fever can get heart disease (especially mitral valve regurgitation), arthritis, and/or abnormal movements known as Sydenham's chorea or Tourette syndrome.
In PANDAS, it is believed that something very similar to Tourette syndrome occurs. One part of the brain that is affected in PANDAS is the basal ganglia, which is believed to be responsible for movement and behavior. Thus, the antibodies interact with the brain to cause tics and/or OCD, instead of Tourette syndrome.