Patients with Lyme disease, that is, active infection with Borrelia burgdorferi, experience many types of musculoskeletal complaints, with different explanatory mechanisms. Appropriate therapy depends on understanding the underlying cause of the complaint and addressing that specific root cause. In the case of active infection the dosage, duration, drug, and method of administration of antibiotics should be determined by the state of the infection and history of prior therapy, according to the established and validated recommendations of the Infectious Disease Society of America. Many patients have musculoskeletal complaints not attributable to active infection; some patients have residual complaints following a documented infection that has been adequately treated with antibiotics previously, and others never had true B. burgdorferi infection in the first place. For such patients, antibiotics are not warranted and in fact may be physically and emotionally harmful. Complaints following an episode of Lyme disease are not necessarily due to ongoing infection, especially adequately treated. Consideration of other diagnoses may suggest use of other effective modalities, including physical therapy and emotional support. Appropriate ordering and interpretation of the various validated seroconfirmatory tests available to study B. burgdorferi infection are critical, as these tests are often misapplied and misconstrued in pursuit of strategies aimed at eliminating patients' suffering. Although seronegative Lyme disease has been reported, seronegativity in a reputable laboratory makes the likelihood of Lyme arthritis very low. On the other hand, a positive result from certain unvalidated laboratories or novel assays proves nothing and should not be viewed as substantiating the diagnosis.