Numerous nonneoplastic conditions of the lungs may result in atypical cells in bronchoalveolar lavage (BAL) specimens mimicking malignant neoplasms. Bone marrow transplant (BMT) recipients have many predisposing factors that would lead to atypical cells in BAL specimens, presenting diagnostic challenges. We reviewed BAL specimens from BMT recipients and correlated our findings with clinical information. During a 5.5-year period, 21 BMT recipients had atypical cells in 27 BAL specimens at Fairview-University Medical Center, Minneapolis, MN. The atypical cells had the cytologic features of squamous or glandular cells. The nuclear/cytoplasmic ratio, atypical cells per case, and background varied from case to case. Most of the patients had 1 or more of the clinical findings that would lead to atypia in BAL specimens: 13 had recent cytoreductive treatment, 9 had positive cultures, and 7 had graft-vs-host disease. There was substantial overlap between the reactive atypia and carcinoma. Clinical correlation was the most important factor in making accurate diagnosis.