Background: This study examined psychiatric comorbidity in adolescents with a gender identity disorder (GID). We focused on its relation to gender, type of GID diagnosis and eligibility for medical interventions (puberty suppression and cross-sex hormones). Methods: To ascertain DSM-IV diagnoses, the Diagnostic Interview Schedule for Children (DISC) was administered to parents of 105 gender dysphoric adolescents. Results: 67.6% had no concurrent psychiatric disorder. Anxiety disorders occurred in 21%, mood disorders in 12.4% and disruptive disorders in 11.4% of the adolescents. Compared with natal females (n = 52), natal males (n = 53) suffered more often from two or more comorbid diagnoses (22.6% vs. 7.7%, p = 0.03), mood disorders (20.8% vs. 3.8%, p = 0.008) and social anxiety disorder (15.1% vs. 3.8%, p = 0.049). Adolescents with GID considered to be "delayed eligible" for medical treatment were older [15.6 years (SD = 1.6) vs. 14.1 years (SD = 2.2), p = 0.001], their intelligence was lower [91.6 (SD = 12.4) vs. 99.1 (SD = 12.8), p = 0.011] and a lower percentage was living with both parents (23% vs. 64%, p less than 0.001). Although the two groups did not differ in the prevalence of psychiatric comorbidity, the respective odds ratios ("delayed eligible" adolescents vs. "immediately eligible" adolescents) were greater than 1.0 for all psychiatric diagnoses except specific phobia. Conclusions: Despite the suffering resulting from the incongruence between experienced and assigned gender at the start of puberty, the majority of gender dysphoric adolescents do not have co-occurring psychiatric problems. Delayed eligibility for medical interventions is associated with psychiatric comorbidity although other factors are of importance as well.