Pulmonary complications (PCs) are a significant cause of morbidity and mortality in hematopoietic stem cell transplant (HSCT) recipients. Pulmonary infiltrates in such patients pose a major challenge for clinicians because of the wide differential diagnosis of infectious and noninfectious conditions. It is rare for the diagnosis to be made by chest radiograph, and commonly these patients will need further invasive and noninvasive studies to confirm the etiology of the pulmonary infiltrates. Aim The aim of this research was to study the pattern of lower respiratory tract infection within the first year after HSCT. Patients and methods This is a prospective study of 60 patients receiving HSCT (because of hematological and nonhematological malignancy) at Kuwait Cancer Center within the first year after transplantation for any suspicious respiratory tract infection. Patients were subjected to sputum and blood examination along with bronchoscopic examination and bronchoalveolar lavage if indicated, and all samples were subjected to microbiological examination for diagnosis of the causative organism. Results Sixty patients were studied for PCs either infectious or noninfectious within the first year after HSCT. The most common complications were infectious complications (70%). Severe PCs were the main causes of death in 13 (21.6%) cases. The PCs were more common and recurrent in allogeneic bone marrow transplantation (BMT) recipients, in whom PCs contributed to death in 12 cases. Bacterial infection, pulmonary edema, and diffuse alveolar hemorrhage were seen more in the early post-BMT period (<100 days), whereas viral, fungal infection, graft-versus-host disease, and bronchiolitis obliterans were seen more in the late post-BMT period (>100 days). Conclusion Lower respiratory tract infection is a serious complication after BMT transplantation. Mixed bacterial and opportunistic infections are the most common etiologies. Pulmonary infiltrates in such patients pose a wide differential diagnosis of infectious and noninfectious conditions. PCs are a significant causes of death in BMT recipients. Egypt J Bronchol 2018 12:233–239 © 2018 Egyptian Journal of Bronchology Egyptian Journal of Bronchology 2018 12:233–239 Keywords: hematopoietic stem cell transplantation, lower respiratory tract infection, pulmonary complications Departments of, aChest Diseases and Tuberculosis, bTropical, Faculty of Medicine, Zagazig University, Zagazig, cInternal Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt Correspondence to Amal Abd El-Azem Sadon, MD, Chest Diseases and Tuberculosis Department, Faculty of Medicine, Zagazig University, Zagazig, 44511, Egypt. Tel: 00201118686807; e-mail: amalsadon@yahoo.com