We retrospectively reviewed all positive Pneumocystis carinii findings among adult patients who had received an allogeneic BM transplant at the Helsinki University Central Hospital between July 1990 and December 1993. The aim was to define the incidence of late onset Pneumocystis carinii pneumonia (PCP) in BMT patients who had routinely received PCP prophylaxis for 6 months post-BMT. In 110 BMT patients, 16 episodes of PCP were documented. Only one patient had been receiving PCP prophylaxis at the onset of PCP. Fourteen of the episodes occurred more than 6 months post-BMT. (median 10.5, range 4-42 months); three of them beyond 1 year. All three had extensive chronic GVHD. Of the 11 patients with an onset between 7-12 months post-BMT, all but one were on methylpredisolone because of chronic GVHD (n = 7) or cytopenia (n = 2) and five of them were in relapse of their hematological malignancy. No mortality from PCP was detected. The risk of developing PCP between 7-12 months post-BMT among patients at risk was 13.4%. We conclude that PCP prophylaxis should be continued until 1 year post-BMT in patients receiving corticosteroid treatment as well as in those with a hematological relapse. Long-term prophylaxis beyond 1 year should be considered in cases with extensive chronic GVHD.