The aim of the study was to determine the incidence and prevalence of hypothyroidism (HT) among childhood cancer survivors by means of register linkage. Patients extracted from the Finnish Cancer Registry data base (5,180 patients with cancer diagnosis at the age of 0-15 years, and born after 1970) were linked with thyroxin reimbursement data (Drug Reimbursement Register) and with thyroxin purchase data (prescription database) maintained by the Social Insurance Institution. At the end of follow-up, the prevalence of HT (10,509/100,000) was found to exceed that in the general population (240/100,000) for those aged <35 years. Diagnostic group (p < 0.0001) and gender (p < 0.0025) had significant effect on the risk of developing HT. Males were less prone to the development of HT. Cumulative incidence rate of HT was highest in patients with thyroid cancer (TC), Hodgkin lymphoma, central nervous system (CNS) tumors and neuroblastoma. Except in patients with TC (4.5 months) and CNS tumors (19 months), the median time for the appearance of HT was quite long, varying between 2 and 4.5 years. We consider our results valuable in providing new data for the planning of thyroid function follow-up in different diagnostic groups of childhood cancer survivors.