The incidence and risk factors for thyroid disorders among adult survivors of allogeneic hematopoietic stem cell transplantation (alloHCT) is not well known. This study evaluated incidence and risk factors of thyroid dysfunction in 259 adult alloHCT recipients who had survived for 2 years or more after transplant. Median follow-up was 4.6 years (range; 2.3 to 15.4 years). The 5-year cumulative incidence of thyroid dysfunction was 30.5% (79 of 259 patients). Majority of thyroid abnormalities were observed beyond 2 years after alloHCT. Subclinical hypothyroidism was the most common thyroid abnormalities accounting for 89% of cases (71 patients). Among these, treatment with thyroid replacement was eventually started in 44% (31 patients). Based on the multivariate analysis, thyroid abnormality was more likely in patients who received high-dose (≥12 Gy) total body irradiation (TBI)-based conditioning regimen compare to low-dose TBI-based (≤500 cGy) and non-TBI-conditioning regimen (p = 0.032). This risk was further augmented directly proportional with the time from alloHCT. These data identify high-dose TBI-conditioning regimen as a risk factor for thyroid dysfunction in adult recipients of alloHCT.