The aim of this study was to investigate the presence of emotional disturbance among Japanese graduate students and the underlying factors of their emotional disturbance. We conducted a cross sectional survey using the Japanese version of the 30-item General Health Questionnaire at 31 graduate schools from 12 university campuses in and around Kyoto, Japan and analyzed the data of 219 graduate students, aged 22-39 years (158 males and 61 females). The rate of emotional disturbance was 53% in the graduate student sample. Graduate students' emotional disturbance was best characterized with four factors: (1) anxiety and insomnia; (2) social dysfunction; (3) depression; and (4) feelings of incompetence. These findings indicate that emotional disturbance among graduate students is prevalent. As mental illness continues to be stigmatized in Japan, to tackle graduate students' emotional disturbance, we propose that besides traditional non-anonymous help (face-to-face counseling services) graduate schools should implement more anonymous help (Internet homepage, e-counseling, crisis line). (Contains 1 table.)