The risk of hypothyroidism after reduced-intensity hematopoietic cell transplantation (HCT) is not well known. We studied the incidence of hypothyroidism among a cohort of HCT recipients who had survived for ≥1 year and received a TBI-based myeloablative (MA) (N = 84) or reduced-intensity (N = 97) conditioning (RIC) regimen. MA HCT recipients were younger at the time of transplant (median age 37 vs 54 years, P < 0.01), otherwise the two groups were comparable. Median follow-up was 28 (range, 12-75) months for MA and 25 (range, 12-67) months for RIC group. The 3-year cumulative incidence of hypothyroidism was 8 and 5%, respectively (P = 0.41). In multivariate analysis, both types of conditioning regimens were associated with similar risks for hypothyroidism (relative risk for MA 1.6 vs RIC). At least in the first few years after HCT, the risks for hypothyroidism are similar among patients receiving TBI-based MA and reduced-intensity regimens.