The intake of total aflatoxins (AFT) and aflatoxin B1 (AFB1) from food in Japan was estimated from AFT and AFB1 concentration and frequency data in 24 foods (884 samples) from a 3-year retail market survey from the summer of 2004 to the winter of 2006, and by food consumption data from the National Health and Nutrition Survey performed in 2005. The AFT and AFB1 survey revealed that peanut, peanut products, cocoa, chocolate, pistachio, white pepper, red pepper, almond, job's tears, buckwheat and corn grits are considered to be contributors of AFT (or AFB1) intake in Japan (maximum AFB1 (AFT) levels ranged from 0.21 to 28.0 µg kg−1 (from 0.21 to 9.0 µg kg−1)) in AFT-contaminated food. A probabilistic approach using the Monte Carlo method was carried out to simulate an estimate of the AFT (or AFB1) intake distributions in each age group in Japan. In this study, AFB1 intake ranged from 0.003 to 0.004 ng kg−1 body weight day−1 (from lower to upper limits), and the potential risk for cancer using a formula devised by the Joint Food and Agricultural Organization/World Health Organization (FAO/WHO) Expert Committee on Food Additives (JECFA) was estimated at 0.00004–0.00005 person/year/100,000 persons, even though this was in the higher levels (95.0th percentile) of the consumer population. The results suggest that the current dietary intake of AFB1 in Japan has no appreciable effect on health.