Abstract: Objective To observe the effect of pulmonary infection on hematopoietic stem cell transplantation. Methods Effect of hematopoietic stem cell transplantation on pulmonary infection in 21 patients with hematopathy admitted to our hospital from August 1999 to March 2012 was retrospectively analyzed.Of these 21 patients, 7 were diagnosed as acute lymphocytic leukemia, 10 as acute non-lymphocytic leukemia, 2 as myeloproliferative syndrome, and 2 as acute aplastic anemia, and 20 received allogeneic hematopoietic stem cell transplantation and 1 received autologous hematopoietic stem cell transplantation. All the patients were diagnosed as deep fungal infection or mixed infection and underwent hematopoietic stem cell transplantation when their lesions disappeared or became smaller after anti-fungal therapy. Results Twenty-eight days after hematopoietic stem cell transplantation, the bone marrow proliferated actively in the 21 patients with their myelopathy completely alleviated. The chimera was 100% donor type after allogeneic hematopoietic stem cell transplantation. Fourteen days after hematopoietic stem cell transplantation, no new pulmonary infection occurred in 14 patients with 1 died of recurrent leukemia, pulmonary infection was exacerbated in 7 patients with 2 completely cured, 3 significantly improved after antifungal therapy for 1-2 months and 2 died due to exacerbated pulmonary infection. Conclusion Hemapathy patients with pulmonary infection can undergo hematopoietic stem cell transplantation after effective anti-infection treatment. Pulmonary fungal infection shows no significant effect on hematopoietic stem cell transplantation.