Pneumocystis jirovecci (PJ) is ubiquitously present in the environment and capable of causing an interstitial pneumonia in immunocompromised subjects. It has been advocated that routine prophylaxis against PJ be given to patients with autoimmune neuromuscular conditions which require prolonged usage of corticosteroid therapy and/or other immunosuppressive agents. Available data, however, suggest that the risk of PJ infection in patients with autoimmune neuromuscular diseases is extremely low and a widespread usage of prophylactic therapy is likely unnecessary. Comorbidities including intestinal lung disease, prolonged lymphopenia, low CD4 count, parenchymal organ failure, and active cancer status appear to increase risk for PJ infection, and it is our opinion that these risk factors should be considered to determine the risk of PJ infection and the requirement for prophylaxis.