The aim of this study was to determine whether prophylactic azithromycin treatment prevents bronchiolitis obliterans syndrome (BOS) after hematopoietic stem cell transplantation (HCT). A series of 1187 patients who underwent HCT between December 1993 and November 2013 at our tertiary referral center in South Korea were enrolled. The median age of these patients was 39.0 years, and 668 (56.3 %) were men. Acute leukemia was the most common indication for HCT. During a median follow-up of 30.7 months after HCT, BOS was diagnosed in 82 patients (6.9 %) at a median of 12.3 months after HCT. One hundred patients received prophylactic azithromycin, of whom 12 developed BOS. BOS was significantly more frequent in patients who were treated with than without prophylactic azithromycin (12.0 versus 6.4 %, P = 0.036). Multivariate analysis revealed that a busulfan-based conditioning regimen (HR 2.73, 95 % CI 1.66-6.45) was the only independent predictor of BOS. The prophylactic use of azithromycin was not associated with the development of BOS by multivariate analysis. Although the present study had some limitations such as its non-randomized retrospective design, differences in baseline patient characteristics between the two groups, and the preference for azithromycin use at our hospital, our findings suggest that prophylactic azithromycin seems to not prevent the development of BOS in HCT recipients.