The epidemiology of reported food-borne disease (FBD) outbreaks from 2001 to 2008 in Korea and Japan were compared in this study. The outbreak rate of FBD in Japan was significantly higher although the average number of patient in each outbreak in Korea was much higher. In both countries, summer was the season when most FBD outbreaks occurred. The comparison study revealed that FBD outbreaks in spring were more frequent in Korea, and outbreaks in winter were more frequent in Japan. Almost half of FBD outbreaks were observed at restaurants in both countries while FBD outbreaks at schools and work-places in Korea were much higher than in Japan. The most frequent cause of bacterial FBDs in Korea was pathogenic Escherichia coli followed by Salmonella species. On the other hand, Campylobacter jejuni was the most frequent source of bacterial FBDs in Japan. Norovirus, which is related to uncontrolled hand hygiene and involvement of ill food workers, was the main cause of viral FBDs in both countries. In conclusion, there are common epidemiological characteristics as well as several differences in FBD outbreaks of Korea and Japan. These are suggested to be originated from the characteristic of climate, food sources, and life styles in two countries. Establishment of stricter control and surveillance system for FBD outbreaks are required for prevention and reduction of FBD outbreaks in both countries.