Children who undergo bone marrow transplantation (BMT) are at risk for Pneumocystis carinii pneumonia (PCP). Prophylaxis using trimethoprim/sulfamethoxazole (TMP/SMX) is highly effective but the incidence of adverse drug reactions is significant. We retrospectively reviewed 33 pediatric BMT (25 allogeneic and eight autologous) in whom dapsone was used for PCP prophylaxis because patients were unable to receive TMP/SMX. Dapsone was administered at 50 mg/m2 p.o. once a week from engraftment to 180 days post-autologous BMT, and to 1 year or throughout the duration of immunosuppressive treatment post-allogeneic BMT. With a total of 7268 patient days of dapsone prophylaxis and a median follow-up of 353 days post-BMT, no proven PCP was diagnosed. Sixteen cases of chest radiograph abnormalities were noted in this patient population but none was attributed to PCP. Dapsone was well tolerated by all children with no serious adverse effects; however, one patient developed Toxoplasma gondii encephalitis during dapsone prophylaxis. Dapsone warrants further evaluation as an alternative for PCP prophylaxis in pediatric BMT patients intolerant of TMP/SMX. Additional prophylaxis should be considered for patients at high risk for T. gondii encephalitis.