PURPOSE: Adolescence is a phase when young people begin to explore their gender identity. Adolescents who identify as a gender minority are vulnerable to experiencing mental health problems due to stigmatization of their identity. METHODS: A population-wide study compared gender minority and cisgender students (aged 13-14 years) self-reported symptoms of probable depression, anxiety, and conduct disorder, and auditory hallucinations, including the distress and frequency of hallucinations. RESULTS: Gender minority students compared to cisgender students had four times the odds of reporting a probable depressive disorder, anxiety disorder, auditory hallucinations, but not conduct disorder. Of those who reported a hallucination, gender minority students were more likely to report hearing them daily but were no more likely to find them distressing. DISCUSSION: Gender minority students experience a disproportionate burden of mental health problems. Services and programming should be adapted to better support gender minority high-school students.