Epidemiologic studies using clinical indicators are limited in the assessment of the biological effects of low-dose ionizing radiation for medical purposes. We evaluated the biological effect of low-dose radiation by comparing translocation frequencies in patients with repeated computed tomography (CT) exposure and CT-naïve patients. The goal of this prospective case-control study was to determine whether repeated CT exposure is associated with increased frequency in chromosomal translocations. Two cohorts, comprised of case patients with a history of repeated CT exposure and age- and sex-matched CT-naïve control patients (n = 48 per cohort), were consecutively enrolled in this single-institution study. CT-radiation exposure was estimated using dose-length products, and translocation frequencies of peripheral blood lymphocytes were assessed using whole chromosome paints by fluorescence in situ hybridization (FISH). Comparison of translocation frequencies between cases and controls was performed using the Wilcoxon rank sum test (paired samples), and the relationship between cumulative radiation exposure and translocation frequency was assessed using a partial correlation analysis. Translocation frequencies were significantly different between cases and controls (P = 0.0003). The median translocation frequency was 7 [95% confidence interval (CI): 6, 8] for cases and 4 (95% CI: 3, 6) for controls. By using cumulative radiation exposure as the effect variable and translocation frequency as the response variable, we found a significant correlation between cumulative radiation exposure and translocation frequency (r = 0.6579, P < 0.0001). Chromosomal translocations were more frequent with repeated CT-exposed patients than in CT-naïve patients, and a positive dose-response relationship was present between cumulative radiation exposure and translocation frequency.