Background: Although the Eating Disorder Examination Questionnaire version 6.0 (EDE-Q) is one of the most widely used questionnaires for eating disorders in Western countries, no research has addressed the psychometric properties of the EDE-Q in a Japanese sample. Methods: We explored the factor structure of the EDE-Q and examined the internal consistency of the derived scales for Japanese participants (Study I), the convergent validity with other eating disorder-related psychological measures (Study II) and the distinction between the derived two body image-related factors with psychological measures (StudyIII). The EDE-Q was administered to 1,430 undergraduate students in Study I and in Study II was subsequently assessed by two self-report measures of eating pathology, the Eating Attitudes Test (EAT-26) for 558 undergraduate students and the Eating Disorders Inventory-II (EDI-II) 111. In StudyIII, another 225 undergraduate students participated in an examination of the relationships of the derived body image-related subscales of the EDE-Q with the psychological measures of the Rosenberg Self-Esteem Scale, Beck Depression Inventory, Public Self-Consciousness Scale, and Multidimensional Perfectionism Scale. Results: Exploratory factor analysis of the EDE-Q identified four meaningful factors. Of the original four EDE-Q factors, "Restriction" and "Eating Concern" were retained. However, the other two factors, "Shape" and "Weight" Concerns, were combined into two different factors: "Fear of Obesity" and "Self-Esteem Based on Shape and Weight". Internal consistency of the derived four factors was adequate, and the relationships with EDI-II and EAT-26 measures demonstrated convergent validity. Analysis of the distinction between "Fear of Obesity" and "Self-Esteem Based on Shape and Weight" revealed that only "Self-Esteem Based on Shape and Weight" was significantly associated with the measures assessing psychopathology related to eating disorders. Conclusions: This study describes restructured factors of the EDE-Q that were tested with undergraduate students. The distinction between two factors, "Fear of Obesity" and "Self-Esteem Based on Shape and Weight", may further the understanding of the psychopathology of the eating disorders of adolescent Japanese subjects to facilitate future developments in research and treatment.