Reports on the occurrence and treatment of heterotopic ossification in amputees are rare. Heterotopic ossification in the residual limbs of amputees may cause pain and skin breakdown and complicate or prevent optimal prosthetic fitting and utilization. Basic science research has shed light on the cellular and molecular basis for this disease process, but many questions remain unanswered. The recent experience of the military amputee centers with traumatic and combat-related amputations has demonstrated a surprisingly high prevalence of heterotopic ossification in residual limbs. Primary prophylactic regimens, such as nonsteroidal anti-inflammatory drugs and local irradiation, which have proved to be effective in preventing and limiting heterotopic ossification in other patient populations, have not been studied in amputees and generally are not feasible in the setting of acute traumatic amputation. When nonsurgical measures such as activity and repeated prosthetic modifications fail to provide relief, surgical excision has provided good early clinical results, with low rates of recurrence and acceptable complication rates in military amputees.