People with an incongruent gender identity are over four times more likely than the general population to suffer from mental health problems.
This finding, from an American campus survey , found that gender minority status was associated with “4.3 times higher odds of having at least 1 mental health problem.” Similarly, a Journal of Sex and Marital Therapy article  notes that “a large percentage of adolescents referred for gender dysphoria have a substantial co-occurring history of psychosocial and psychological vulnerability.”
In Lisa Littman’s seminal work  on rapid onset gender dysphoria, 62.5% of the young people whose parents were surveyed had at least one mental health or neurodevelopmental issue. 58.0% had a poor or extremely poor ability to handle negative emotions productively; 61.4% were overwhelmed by strong emotions and tried to avoid (or went to great lengths to avoid) experiencing them.
In a systematic review  of individuals diagnosed with gender dysphoria, 53.2% had at least one mental disorder in their lifetime. Such figures substantially exceed prevalence rates of comorbid psychopathology in the general population : a further paper  studying hospital encounters found that the prevalence of mental disorder diagnoses was higher in transgender encounters (77%) than in the general population (37.8%).
A Swedish study  found that sex-reassigned persons had a higher risk of inpatient care for a psychiatric disorder (other than gender identity disorder) than the control population. Inpatient care for psychiatric disorders was also significantly more common among sex-reassigned persons than among controls, both before and after sex reassignment.
 Lipson, S. K., Raifman, J., Abelson, S. & Reisner, S. L. (2019). Gender Minority Mental Health in the U.S.: Results of a National Survey on College Campuses. American Journal of Preventive Medicine 57 (3): 293-301. [Link]
 Bechard, M., VanderLaan, D. P., Wood, H., Wasserman, L. & Zucker, K. (2017). Psychosocial and Psychological Vulnerability in Adolescents with Gender Dysphoria: A “Proof of Principle” Study. Journal of Sex & Marital Therapy 43 (7). [Link]
 Littman, L. (2018). Rapid-onset gender dysphoria in adolescents and young adults: A study of parental reports. PLOS ONE, 13 (8). [Link]
 de Freitas, L. D., Léda-Rêgo, G., Bezerra-Filho, S., & Miranda-Scippa, Â. (2020). Psychiatric disorders in individuals diagnosed with gender dysphoria: A systematic review. Psychiatry and Clinical Neurosciences, 74 (2), 99–104. [Link]
 Zucker, K.J., Lawrence, A.A., Kreukels, B.P. (2016). Gender Dysphoria in Adults. Annu Rev Clin Psychol. 12: 217-47. [Link]
 Bishoy, H., Repack, D., Tarang, P., Guirguis, E., Kumar, G. & Sachdeva, R. (2019). Psychiatric disorders in the U.S. transgender population. Annals of Epidemiology 39: 1-7. [Link]
 Dhejne, C., Lichtenstein, P., Boman, M., Johansson, A. L. V., Långström, N., & Landén, M. (2011). Long-term follow-up of transsexual persons undergoing sex reassignment surgery: Cohort study in Sweden. PLoS ONE, 6(2). [Link]