FFQ, the primary method of dietary assessment in large-scale nutritional epidemiological studies, preclude an informed evaluation of the timing of dietary intake and meal-specific dietary intake. In this study, we developed the Meal-based Diet History Questionnaire (MDHQ), a self-administered questionnaire designed for estimating food and nutrient intakes for each meal type separately. The development was done based on a 16-d dietary record obtained from 242 Japanese adults. The MDHQ consisted of the three different parts, with a total of 196 items. Part 1 of the MDHQ asks about consumption frequency of generic food groups (n 24) for each meal type: breakfast, morning snack, lunch, afternoon snack, dinner and night snack. Part 2 of the MDHQ asks about relative consumption frequency of sub-food groups within one of the generic food groups which are asked in Part 1. Combining information derived from Parts 1 and 2 enables us to increase the number of foods we can estimate efficiently but within a limited number of questions. Part 3 of the MDHQ asks about general eating behaviours, which are intended to use in a variety of ways during dietary intake calculation. A series of calculation algorithms for food groups, energy and nutrients was also prepared. Given that the MDHQ was empirically developed based on comprehensive information on actual food consumption, this innovative tool may be promising for future epidemiological research on meal patterns and time of day of dietary intake, or chrono-nutrition research. A rigorous evaluation of validity of the MDHQ is warranted.