To examine the late effects and health-related quality of life of childhood cancer survivors (CCS) after radiotherapy (RT), we performed a cross-sectional survey using self-rating questionnaires. The subjects were divided into 3 groups: CCS treated with or without RT, and a general population matched for age, gender, residential area, and work status. The numbers in each group were 113, 72, and 1,000, respectively. The median ages of CCS at diagnosis and the time of the survey were 8 and 22 years, respectively. The mean final heights of males and females were significantly lower in CCS with RT than in the other 2 groups. Risk factors for a short stature were total body irradiation (TBI) [odds ratio (OR) 17.8, p < 0.001], spinal irradiation (OR 8.31, p = 0.033), and an age younger than 10 years at diagnosis. Late effects were observed in 68% of CCS with RT compared with 36% of CCS without RT. Multivariate analysis revealed that TBI was significantly associated with endocrine dysfunction (OR 12.3), skull and spinal irradiation with cognitive dysfunction (OR 16.1 and 11.5, respectively), and spinal irradiation with a short stature (OR 14.1), respectively. Physical dysfunction, psychological stress, and problems of social adaptation were observed in >50% of CCS with RT.