A retrospective study included 134 pediatric patients after allogeneic hematopoietic stem cell transplantation, divided into groups with bronchiolitis obliterans syndrome (BOS) and without BOS. Risk factors for BOS were ABO incompatibility, HLA mismatch, pulmonary infection within 100 days after transplantation, cytomegalovirus serologic positivity, and immunoglobulin IgA deficiency before transplantation. After transplantation, IgA and IgM levels dropped significantly, with many patients having values below reference limits. Pre-transplantation serum IgA levels were lower in the BOS group compared to the non-BOS group. In multivariate binary logistic and Cox regression models, pre-transplant IgA deficiency was confirmed as an independent risk factor for BOS. The study hypothesizes that the decrease in immunoglobulins after transplantation contributes to the weakening of the respiratory mucosal defenses and the development of BOS.