To elucidate the prevalence of lesbian, gay, bisexual, and transgender (LGBT) among Japanese youth, we conducted a survey research that targeted university students. Participants were first-year students (n=1597) at Ibaraki University, Japan (Phase 1 study) or second- to fourth-year students (n=944) at the university who were randomly preferred in the survey (Phase 2 study). Surveys measured gender identity and sexual orientation, partly using the gender identity scale (GIS). The prevalence of LGBT youth among university students were 2.7%, 0.5%, 5.3%, and 0.8% (Phase 1 study) or 1.4% (Phase 2 study), respectively. The GIS scores of the transgender group were significantly lower than those of the female, male, and LGB groups (p<0.01). This is the first to clarify the prevalence of LGBT among youth in Japan. It has been suggested that such individuals in Japan, as in other countries, are at risk for physical and mental health concerns, thereby necessitating social and medical intervention. Further investigation in these areas will be needed.