While completing their degree courses, graduate students often complain about poor sleep and mental health, which is mainly caused by the academic environment and the uncertainty of their success in obtaining their degree. To estimate the prevalence of sleep disturbances among them and the related adverse consequences, we conducted a cross-sectional epidemiological survey at 12 university graduate schools in Kyoto, Japan. A total of 241 responses were returned (44%) and the data of 219 graduate students, representing 0.1% of the total number of Japanese graduate students in Japan (158 males and 61 females, aged 22–39 years), were analyzed. Participants completed the self-reported Pittsburgh Sleep Quality Index questionnaire, together with specific questions designed for the purpose of the study. Among graduate students, 29.8% reported fatigue, 9.6% health problems, 5% university absenteeism, and 3.2% accidents at their university as adverse consequences of their sleep problems. The prevalence rate of excessive daytime sleepiness was 4.1% in this study, lower than the reported rate in the general young adult population. The prevalence rates of other sleep disturbances were similar to the reported rates for the general young adult population; we consequently suggest that the prevalence rates of the adverse consequences of sleep problems are higher for the general young adult population than for the less sleepier graduate students. Graduate students also reported a low consultation rate for sleep problems despite high prevalence rates of adverse consequences, indicating the need to increase awareness of sleep problems and their prevention among them.