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We evaluated the incidence and risk factors for hypogammaglobulinemia after allogeneic hematopoietic SCT (HSCT) in pediatric patients. Ig levels were measured pre-transplant, every 2 weeks until day 100 and then monthly post SCT in 185 patients undergoing myeloablative HSCT. Median age was 9 years; 142 (77%) had malignant disease and 114 (62%) received stem cells from an unrelated source. Hypogammaglobulinemia (IgG <500 mg/dL) developed in 143 (77%) of the patients at a median of 56 days (range 15-339) post SCT. The cumulative incidence of hypogammaglobulinemia at 1 year was higher among patients who developed acute GVHD (97% vs 54%, P<0.001), and for those receiving stem cells from an unrelated source (94% vs 51%, P<0.001). The cumulative incidence of TRM was significantly higher for patients with hypogammaglobulinemia (P=0.026). In multivariable analysis, lower pre-transplant IgG level (P<0.001), younger age (P=0.012), diagnosis of malignant disease (P<0.001), receiving unrelated SCT (P<0.001) and development of acute GVHD (P<0.001) were all significantly associated with higher risk of hypogammaglobulinemia post HSCT. We conclude that hypogammaglobulinemia is common, following allogeneic HSCT in pediatric patients, especially in those with malignant diseases, those who receive an unrelated transplant or patients who develop GVHD.