Aim To investigate the frequency of calcification in the basal ganglia and the dentate nuclei in the cerebellum, and compare the difference in age and area, we examined the brain computed tomography (CT) images of all patients in two representative university hospitals in Japan. Methods We examined the brain CT images of 2526 patients in Gifu University Hospital (UH) and 2573 patients in Niigata UH. These patients were examined in these hospitals from October 2009 to September 2010. Results Punctate calcification of the basal ganglia was observed in 435 of 2526 patients (17.2%) in Gifu UH and 530 of 2573 patients (20.6%) in Niigata UH. The frequency of calcification increased with age. Patchy calcification of the basal ganglia was observed in 32 (1.3%) and 50 patients (1.9%) in Gifu UH and Niigata UH, respectively. Among patients aged over 65 years, 24 (2.1%) and 34 (3.1%) patients showed patchy calcification in Gifu UH and Niigata UH, respectively. Calcification of the cerebellar dentate nuclei was detected in just seven and four patients in Gifu UH and Niigata UH, respectively. Conclusion Compared with previous reports, the frequency of calcification of the basal ganglia in this study markedly increased. This might be because of the increased number of older adults and the increased sensitivity of CT. Geriatr Gerontol Int 2013; 13: 706–710.