This study had the following aims: to perform a multidimensional, multi-method assessment of the food choice motivations of Japanese university students, to identify subgroups among them that shared similar food choice motivations, and to determine if those groups could be distinguished from each other based on personal characteristics, eating habits, and health information behaviors. The data collection phase consisted of two parts: a limited number of semi-structured interviews used to adapt a questionnaire survey for use with a Japanese population, and a questionnaire survey. Factor analysis of the survey responses revealed seven factors: consumption experience, convenience, health, weight control, content, familiarity and price. Cluster analysis of the factor scores for each student generated five subgroups. Chi-square tests and univariate ANOVA demonstrated that differences between the groups existed in terms of gender, living situation, snack and fruit consumption, desire to change eating habits, information use and trust of health information sources. Based on the results of this study, recommendations concerning nutrition education for Japanese university students, targeted interventions for particular subgroups, and implications for the Food Choice Questionnaire as a multidimensional assessment of food motivations are discussed