To estimate the human health burden of foodborne infections caused by Campylobacter, Salmonella, and Vibrio parahaemolyticus in Japan, an epidemiological study was conducted in Miyagi Prefecture. Laboratory-confirmed infections among patients with diarrhea caused by the three pathogens were ascertained from two clinical laboratories in the prefecture from April 2005 to March 2006. To estimate the number of ill persons who were not laboratory-confirmed, we estimated physician-consultation rates for patients with acute diarrhea by analyzing foodborne outbreak investigation data for each pathogen and the frequency at which stool specimens were submitted from a physician survey. Each factor was added to a Monte-Carlo simulation model as a probability distribution, and the number of laboratory-confirmed cases was extrapolated to estimate the total number of ill persons. The estimated incidence of foodborne infections per 100,000 per year in this region estimated by this model was 237 cases for Campylobacter, 32 cases for Salmonella, and 15 cases for V. parahaemolyticus. Simulated results indicate a significant difference between our estimated incidence and the reported cases of food poisoning in this region. An enhanced surveillance system is needed to complement the present passive surveillance on foodborne illnesses in Japan to identify food safety issues more precisely, and to monitor the effectiveness of risk management options.