We describe the clinical course of idiopathic pneumonia diagnosed by lung biopsy after allogeneic marrow transplantation and the associations of clinical presentation with outcome. All allogeneic marrow transplant recipients with an open-lung biopsy at a single marrow transplantation research center between January 1983 and December 1988 who were without infection were reviewed as a case series (n = 41). Data were retrieved from clinical information routinely collected at the time of transplantation on all patients. The onset of pneumonia was 11 to 143 days after transplant (mean 35), and 93% of cases displayed diffuse pulmonary infiltrates. Overall in-hospital mortality was 71% (n = 29). The case fatality rate was 59% (n = 24): 13 patients (32%) died with progressive respiratory failure, and the other 11 fatalities (27%) died either with recurrent respiratory failure after initial improvement (n = 7) or from nonpulmonary causes without resolution of pneumonia (n = 4). Infection was a major complication and was present at autopsy in 11 of 16 cases (69%). Of 12 patients discharged from the hospital 6 died within 1 yr, most commonly with relapse of malignancy. Both receipt of total-body irradiation > 1,200 cGy and presence of acute graft-versus-host disease were associated with an increased rate of resolution of pneumonia. The overall mortality of idiopathic pneumonia after allogeneic marrow transplantation is high, but less than one-third of patients die of progressive respiratory failure related to idiopathic pneumonia. Infection is commonly associated with death in marrow recipients previously diagnosed with idiopathic pneumonia by lung biopsy.(ABSTRACT TRUNCATED AT 250 WORDS)