"Sex reassignment therapy" (SRT) is an umbrella term for all medical treatments related to sex reassignment of both transgender and intersex people.

Individuals make different choices regarding sex reassignment therapy, which may include female-to-male or male-to-female hormone replacement therapy (HRT) to modify secondary sex characteristics, sex reassignment surgery (such as orchiectomy) to alter primary sex characteristics, chest surgery such as top surgery or breast augmentation, or, in the case of trans women, a trachea shave, facial feminization surgery or permanent hair removal.

To obtain sex reassignment therapy, transsexual people are generally required to undergo a psychological evaluation and receive a diagnosis of gender identity disorder in accordance with the Standards of Care (SOC) as published by the World Professional Association for Transgender Health. This assessment is usually accompanied by counseling on issues of adjustment to the desired gender role, effects and risks of medical treatments, and sometimes also by psychological therapy. The SOC are intended as guidelines, not inflexible rules, and are intended to ensure that clients are properly informed and in sound psychological health, and to discourage people from transitioning based on unrealistic expectations.

The American Psychiatric Association permits a diagnosis of "gender dysphoria" if the criteria in the DSM-5 are met. The DSM-5 moved this diagnosis out of the sexual disorders category and into a category of its own. The DSM-5 states that at least two of the criteria for gender dysphoria must be experienced for at least six months' duration in adolescents or adults for diagnosis. The diagnosis was renamed from "Gender Identity Disorder" to "Gender Dysphoria", after criticisms that the former term was stigmatizing. Subtyping by sexual orientation was deleted. The diagnosis for children was separated from that for adults, as "gender dysphoria in children". The creation of a specific diagnosis for children reflects the lesser ability of children to have insight into what they are experiencing, or ability to express it in the event that they have insight.

The International Classification of Diseases (ICD-10) list three diagnostic criteria for "transsexualism" (F64.0): Uncertainty about gender identity which causes anxiety or stress is diagnosed as sexual maturation disorder, according to the ICD-10.

Transsexualism appears in the International Statistical Classification of Diseases and Related Health Problems (ICD, currently in its tenth edition). The ICD-10 incorporates "transsexualism", "dual role transvestism," and "gender identity disorder of childhood" into its gender identity disorder category. It defines transsexualism as "[a] desire to live and be accepted as a member of the opposite sex, usually accompanied by a sense of discomfort with, or inappropriateness of, one's anatomic sex, and a wish to have surgery and hormonal treatment to make one's body as congruent as possible with one's preferred sex."

Historically, transsexualism has also been included in the American Psychiatric Association's "Diagnostic and Statistical Manual of Mental Disorders" (DSM). With the DSM-5, transsexualism was removed as a diagnosis, and a diagnosis of gender dysphoria was created in its place. This change was made to reflect the consensus view by members of the APA that transsexuality is not in and of itself a disorder and that transsexual people should not be stigmatized unnecessarily. By including a diagnosis for gender dysphoria, transsexual people are still able to access medical care through the process of transition.

Similarly, the World Professional Association for Transgender Health (WPATH), and many transsexual people, have recommended the removal of transsexualism from the mental health chapter of the upcoming ICD, ICD-11 (due to be released in 2018). They argue that at least some mental health professionals are being insensitive by labelling transsexualism as "a disease", rather than the inborn trait which those who have it believe it to be. Principle 18 of The Yogyakarta Principles, a document of international human rights law, opposes such diagnosis as mental illness as medical abuse.

The current diagnosis for transsexual people who present themselves for medical treatment is gender dysphoria (leaving out those who have sexual identity disorders without gender concerns). According to the "Standards of care" formulated by the World Professional Association for Transgender Health (WPATH), formerly the Harry Benjamin International Gender Dysphoria Association, this diagnostic label is often necessary to obtain sex reassignment therapy with health insurance coverage, and the designation of gender identity disorders as mental disorders is not a license for stigmatization or for the deprivation of gender patients' civil rights.

The question of whether to counsel young children to be happy with their assigned sex, or to encourage them to continue to exhibit behaviors that do not match their assigned sex—or to explore a transsexual transition—is controversial. Some clinicians report that a significant proportion of young children diagnosed with gender dysphoria later do not exhibit any dysphoria.

Professionals who treat gender identity disorder in children have begun to refer and prescribe hormones, known as a puberty blocker, to delay the onset of puberty until a child is believed to be old enough to make an informed decision on whether hormonal gender reassignment leading to surgical gender reassignment will be in that person's best interest.

Transphobia is a range of negative attitudes, feelings or actions toward transgender or transsexual people, or toward transsexuality. Transphobia can be emotional disgust, fear, violence, anger or discomfort felt or expressed towards people who do not conform to society's gender expectations. It is often expressed alongside homophobic views and hence is often considered an aspect of homophobia. Transphobia is a type of prejudice and discrimination similar to racism and sexism, and transgender people of color are often subjected to all three forms of discrimination at once.

Child victims of transphobia experience harassment, school bullying, and violence in school, foster care, and social programs. Adult victims experience public ridicule, harassment including misgendering, taunts, threats of violence, robbery, and false arrest; many feel unsafe in public. A high percentage report being victims of sexual violence. Some are refused healthcare or suffer workplace discrimination, including being fired for being transgender, or feel under siege by conservative political or religious groups who oppose laws to protect them. There is even discrimination from some people within the movement for the rights of gender and sexual minorities.

Besides the increased risk of violence and other threats, the stress created by transphobia can cause negative emotional consequences which may lead to substance abuse, running away from home (in minors), and a higher rate of suicide.

In the Western world, there have been gradual changes towards the establishment of policies of non-discrimination and equal opportunity. The trend is also taking shape in developing nations. In addition, campaigns regarding the LGBT community are being spread around the world to improve acceptance; the "Stop the Stigma" campaign by the UN is one such development.

Therapeutic approaches for GIDC differ from those used on adults and have included behavior therapy, psychodynamic therapy, group therapy, and parent counseling. Proponents of this intervention seek to reduce gender dysphoria, make children more comfortable with their bodies, lessen ostracism, and reduce the child's psychiatric comorbidity. The majority of therapists currently employ these techniques. "Two short term goals have been discussed in the literature: the reduction or elimination of social ostracism and conflict, and the alleviation of underlying or associated psychopathology. Longer term goals have focused on the prevention of transsexualism and/or homosexuality."

Individual therapy with the child seeks to identify and resolve underlying factors, including familial factors; encourage identification by sex assigned at birth; and encourage same-sex friendships. Parent counseling involves setting limits on the child's cross-gender behavior; encouraging gender-neutral or sex-typical activities; examining familial factors; and examining parental factors such as psychopathology. Longtime researchers of gender identity disorder, Kenneth Zucker and Susan Bradley, state that it has been found that boys with gender identity disorder often have mothers who to an extent reinforced behavior more stereotypical of young girls. They also note that children with gender identity disorder tend to come from families where cross-gender role behavior was not explicitly discouraged. However, they also acknowledge that one could view these findings as merely indicative of the fact that parents who were more accepting of their child's cross-gender role behavior are also more likely to bring their children to a clinical psychiatrist as opposed to parents who are less accepting of cross-gender role behavior in their children (Bradley, Zucker, 1997). " Proponents acknowledge limited data on GIDC: "apart from a series of intrasubject behaviour therapy case reports from the 1970s, one will find not a single randomized controlled treatment trial in the literature" (Zucker 2001). Psychiatrist Domenico Di Ceglie opines that for therapeutic intervention, "efficacy is unclear," and psychologist Bernadette Wren says, "There is little evidence, however, that any psychological treatments have much effect in changing gender identity although some treatment centres continue to promote this as an aim (e.g. Zucker, & Bradley, 1995)." Zucker has stated that "the therapist must rely on the 'clinical wisdom' that has accumulated and to utilize largely untested case formulation conceptual models to inform treatment approaches and decisions."

Children with persistent GID are characterized by more extreme gender dysphoria in childhood than children with desisting gender dysphoria. Some (but not all) gender diverse / gender independent / gender fluid youth will want or need to transition, which may involve social transition (changing dress, name, pronoun), and, for older youth and adolescents, medical transition (hormonal and surgical intervention). Treatment may take the form of puberty blockers such as Lupron Depot or Leuprolide Acetate, or cross-sex hormones (i.e., administering estrogen to an assigned male at birth or testosterone to an assigned female at birth), or surgery (i.e., mastectomies, salphingo-oophorectomies/hysterectomy, the creation of a neophallus in female-to-male transsexuals, orchiectomies, breast augmentation, facial feminization surgery, the creation of a neovagina in male-to-female transsexuals), with the aim of bringing one’s physical body in line with their felt gender. The ability to transition (socially and medically) are sometimes needed in the treatment of gender dysphoria.

The Endocrine Society does not recommend endocrine treatment of prepubertal children because clinical experience suggests that GID can be reliably assessed only after the first signs of puberty. It recommends treating transsexual adolescents by suppressing puberty with puberty blockers until age 16 years old, after which cross-sex hormones may be given.

The University of Washington is leading the largest study of transgender youth ever conducted. The study, known as the Transgender Youth Project, looks at 300 transgender kids between the ages of 3 and 12. Researchers hope to follow the children for 20 years.

During the year prior to the 2015 U.S. survey, 59 percent of respondents reported avoiding using a public restroom out of fear of violence or harassment. 32 percent limited the amount they ate or drink in order to avoid using a public restroom. Eight percent reported suffering a urinary tract infection, kidney infection, or other kidney problem as a result of avoiding public restrooms.

Thirty-three percent reported having negative experiences with a healthcare professional related to being transgender, such as verbal harassment or denial of treatment. 23 percent reported that they did not seek treatment for a condition out of fear of being mistreated, while 33 percent did not seek treatment because they were unable to afford it.

During the month prior to the survey, 39 percent of American transgender people experienced major psychological distress, compared to 5 percent of the general population of the United States. 40 percent had attempted suicide at some point in their life, compared to 4.6 percent of the American population. Family and community support were correlated with far lower rates of suicide attempts and of major psychological distress.

A study conducted on transgender women of color in San Francisco has shown a higher correlation between transphobia and risk of transgender women engaging in HIV risk behavior. The study shows that the transgender youth face social discrimination, and they may not have a social role model. The young adults in this group have shown a higher risk of engaging in unprotected receptive anal intercourse when the exposure to transphobia is high. Therefore, as per the study shows a correlation between transphobia and high risk of HIV.