The objective of this study was to examine temporal and regional variations of sporadic Creutzfeldt-Jakob disease (sCJD) in a retrospective study using Japanese national surveillance data from 2001 to 2010. We calculated the incidence of sCJD by age and sex, derived the standardized incidence in each of the 47 prefectures, and performed spatial disease clustering analysis. The average annual incidence of sCJD was 1.026 per million in men (637 patients) and 1.132 per million in women (733 patients), a significant sex difference after adjustment for age (P = 0.001). The ratios of familial CJD to sCJD apparently increased between 2001-2005 and 2006-2010, possibly as a result of the nationwide introduction of genetic testing after 2006. Based on the data of 2006-2010, certain geographical clusters of sCJD were identified. The incidence of sCJD was higher in several specific prefectures compared to the national average. Thus, sCJD appears to have regional variations, suggesting the existence of genetic or region-specific factors affecting the incidence of the disease.