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Having a transgender identity is not a pathology, although in the past diagnoses such as transsexuality or gender identity disorder existed in the international classification systems for mental disorders, such as the DSM and ICD. In the current DSM-5, gender dysphoria is included as a diagnosis: the experience of distress that may arise in relation to the conflict between the assigned birth gender and gender identity.

Malta depathologised gender identity in 2016 through Act LVI of 2015​ amending the Gender Identity, Gender Expression and Sex Charactistics Act (CAP 540)​. Article 15(2) of this Act states:

The pathologisation of any form of sexual orientation, gender identity and, or gender expression as may be classified under the International Classification of Diseases or any other similar internationally recognised classification, shall be null and void in Malta. The nullity of such classification shall not impact negatively the provision of any healthcare service related to sex and, or gender.

In the ICD-11​, trans-related categories have been removed from the Chapter on Mental and Behavioral Disorders, which means that trans identities are formally de-psycho-pathologized in the ICD-11.

Gender dysphoria must then rather be interpreted as a condition that one suffers temporarily, which can be alleviated by treatment, not as a psychiatric disorder. This interpretation follows the approach of the World Professional Association for Transgender Health (WPATH, 2012) as set out in its Standards of Care 7​. "There is a difference between transgender identity or gender nonconformity and gender dysphoria. Gender non-conformity refers to the extent to which a person's gender identity, role or expression differs from the cultural norms prescribed for people of a certain gender. Gender dysphoria only refers to suffering from the inconsistency between birth gender and gender identity." (SOC7, p. 5) WPATH further emphasises that gender variation is not pathological and should therefore not be classified as a mental disorder (SOC7, p. 4).

Individuals can have a gender-variant identity or expression without this being accompanied by any need for treatment or guidance. When trans persons find a form of treatment necessary, it is primarily intended to decrease their discomfort, but the treatment itself can also be interpreted very individually. What a trans person deems necessary differs greatly from person to person: some find one or more gender-affirming surgeries necessary, for others counselling or hormone therapy is sufficient. There is no such thing as the 'right' trajectory that trans persons must go through in their transition.

Research has shown that so-called 'reparative therapies', with the aim of making the trans person accept their gender assigned at birth, are not effective in reducing distress (Drescher, 2013). Furthermore, this type of practice is now also considered to be unethical and was banned in Malta through the Affirmation of Sexual Orientation, Gender Identity and Gender Expression Act (CAP 567), and has been widely classified as torture or cruel or inhumane treatment in the international human rights framework. Current medical procedures and protocols for psycho-social counselling and gender-affirming treatment have, on the other hand, proved to be very effective in increasing the well-being of trans persons who wish to receive medical treatment (WPATH, 2008). You can find this in the Standards of Care​ of the World Professional Association for Transgender Health (WPATH).