Gender-referred adolescents (GR) have been reported to present with considerable psychiatric symptomatology compared to their age-peers. There is, however, little research on how they compare to adolescents referred due to mental health problems (MHR). We set out to compare psychopathology in adolescents referred to our specialized gender identity unit (n = 84) and adolescents referred to a general adolescent psychiatric clinic (n = 293) in a university hospital setting in Finland. Of the GR adolescents, 40.9% had not received any psychiatric diagnosis during adolescence. Eating disorders were less common in the GR than in the MHR group, but otherwise the prevalences of disorders did not differ statistically significantly. At the symptom level, the GR adolescents displayed significantly more suicidal ideation and talk and less alcohol abuse and eating disorder symptoms than did the MHR adolescents, but otherwise their symptom profiles were comparable. Additionally, the GR adolescents had significantly fewer total externalizing symptoms than did the MHR adolescents. Adolescents seeking gender affirming treatments present with psychiatric symptoms and disorders comparable to those seen among adolescent psychiatric patients. Medical gender affirming care may not be a sufficient intervention for treating psychiatric comorbidities of adolescents with gender dysphoria.