Microsporidia are obligate, intracellular protozoal parasites that can be pathogenic in immunocompromised individuals. The majority of cases of microsporidiosis have been documented in patients with HIV, and only a few case reports exist of infection in solid organ transplant patients. We report the first case of pulmonary microsporidial infection in an allogeneic bone marrow transplant recipient in the US. The patient was a recipient of a T-cell-depleted graft who succumbed to complications from respiratory failure 63 days post transplant. The diagnosis was made post mortem by electron microscopy and confirmed with PCR. Although rare, microsporidial infection should be considered in the differential diagnosis of unexplained pulmonary infection in bone marrow transplant patients.