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Abstract Wiskott Aldrich syndrome (WAS) is a rare disease and hematopoietic stem cell transplant (HCT) is considered the treatment modality of choice for WAS. We conducted a cross-sectional analysis on the KIDS’ pediatric inpatient database and compared hospitalization rates, complications and healthcare utilizations in the transplant and non-transplant arms. Of the 383 pediatric admissions with diagnosis of WAS between 2006–2012, 114 underwent transplant and 269 did not. The non-transplant arm included older children, female patients and more African Americans. Death rates, income and payer source were similar in both arms, however the total charge for each admission was higher in the transplant arm. Emergency room visits were similar but non-elective admissions were more in the non-transplant arm. Length of stay was prolonged in the transplant arm. When comparing morbidities, lymphomas, ulcerative colitis and autoimmune complications of WAS were seen only in the non-transplant arm. Our study shows that transplant is the largest contributor to healthcare utilization in WAS patients. We identified healthcare disparities based on race and socioeconomic status and found that this rare disease is being appropriately directed to centers with HCT expertise. We noted a change in practice moving away from splenectomy in WAS patients.