The frequency of PJP in SLE patients on cyclophosphamide remains low (0.1588%). Therefore, routine use of trimethoprim-sulfamethoxazole for PJP prophylaxis in SLE patients on cyclophosphamide does not appear to be substantiated by this study, except in those with elevated risk, ie, with severe leucopenia, lymphopenia, high dose corticosteroids, hypocomplementemia, active renal disease, and higher mean SLEDAI score. There is a need for consensus guidelines addressing prophylactic antibiotics in these patients.