Thyroid dysfunction is a known complication after hematopoietic cell transplantation (HCT) in children with reports involving relatively short follow-up and small patient numbers. This study involves 791 patients less than 18 years of age at HCT at the Fred Hutchinson Cancer Research Center with follow-up from 1969 through 2007. Thyroid dysfunction continued for 28 years after transplantation. Hypothyroidism was the most common abnormality with other abnormalities of hyperthyroidism and thyroiditis. Multivariate analysis showed that thyroid dysfunction was more likely if patients were less than 10 years of age (P < .001), but there was no difference between receiving a total body irradiation or busulfan based regimens (P = .48) compared with cyclophosphamide conditioning alone (P = .008). Thyroid tumors occurred at a median of 9.9 (4.5-22.3) years after HCT and included 13 with papillary carcinoma and 5 with benign adenomas. Children who receive a HCT should be monitored for thyroid abnormalities throughout life.