Most cases of acute gastroenteritis and foodborne disease are not ascertained by public health surveillance because the ill person does not always seek medical care and submit a stool sample for testing, and the laboratory does not always test for or identify the causative organism. We estimated the total burden of acute gastroenteritis in Miyagi Prefecture, Japan, using data from two 2-week cross-sectional, population-based telephone surveys conducted in 2006 and 2007. To estimate the number of acute gastroenteritis illnesses caused by Campylobacter, Salmonella, and Vibrio parahaemolyticus in Miyagi Prefecture, we determined the number of cases for each pathogen from active laboratory-based surveillance during 2005 to 2006 and adjusted for seeking of medical care and submission of stool specimens by using data from the population-based telephone surveys. Monte Carlo simulation was used to incorporate uncertainty. The prevalence of acute gastroenteritis in the preceding 4 weeks was 3.3% (70 of 2,126) and 3.5% (74 of 2,121) in the winter and summer months, yielding an estimated 44,200 episodes of acute gastroenteritis each year in this region. Among people with acute gastroenteritis, the physician consultation rate was 32.0%, and 10.9% of persons who sought care submitted a stool sample. The estimated numbers of Campylobacter-, Salmonella-, and V. parahaemolyticus -associated episodes of acute gastroenteritis were 1,512, 209, and 100 per 100,000 population per year, respectively, in this region. These estimates are significantly higher than the number of reported cases in surveillance in this region. Cases ascertained from active surveillance were also underrepresented in the present passive surveillance, suggesting that complementary surveillance systems, such as laboratory-based active surveillance in sentinel sites, are needed to monitor food safety in Japan.