Allogeneic bone marrow transplant recipients are prone to pulmonary infections caused by a wide spectrum of organisms. Since the first bone marrow transplatation (BMT) done in 1983 at the Tata Memorial Hospital, we have recently seen the first case of Mycobacterium Fortuitum Chelonae complex among 117 BMT (including 90 allogeneic and 27 autologous) patients. The patient was on immunosuppressants for chronic GVHD post allogeneic BMT done for CML-CP. He developed pulmonary mycobacterial infection 13 months post BMT. Diagnosis was difficult because of the atypical presentation, negative culture reports, and the presence of multiple pathogens due to immunosuppression. In our case the diagnosis was eventually established after examination of material obtained by bronchoscopy. Patient has shown response to antituberculosis drugs after 2 months. This shows the need to consider atypical mycobacterial infection in the differential diagnosis of pulmonary illness in the post allogeneic BMT setting.