Many surgical procedures have been developed to create a neovagina, as none of them is ideal. Surgical intervention should only be considered after non-surgical pressure dilation methods have failed to produce a satisfactory result. Neovaginoplasty can be performed using skin grafts, a segment of bowel, ileum, peritoneum, Interceed, buccal mucosa, amnion, or dura mater. Success of such methods should be determined by sexual function, and not just by vaginal length, as has been done in the past. Ileal or cecal segments may be problematic because of a shorter mesentery, which may produce tension on the neovagina, leading to stenosis. The sigmoid neovagina is thought to be self-lubricating, without the excess mucus production associated with segments of small bowel. Vaginoplasty may create scarring at the introitus (the vaginal opening), which requires additional surgery to correct. Vaginal dilators are required postoperatively to prevent vaginal stenosis from scarring. Other complications include bladder and bowel injuries. Yearly exams are required as neovaginoplasty carries a risk of carcinoma, although carcinoma of the neovagina is uncommon. Neither neovaginoplasty nor vaginal dilation should be performed before puberty.

Flibanserin is the first and only medication approved for women for the treatment of HSDD. It is only slightly effective over placebo, having been found to increase the average number of satisfying sexual events per month by 0.5 to 1. The side effects of dizziness, sleepiness, and nausea occur about three to four times more often. Overall improvement is slight to none.

A few studies suggest that the antidepressant, bupropion, can improve sexual function in women who are not depressed, if they have HSDD. The same is true for the anxiolytic, buspirone, which is a 5-HT receptor agonist similarly to flibanserin.

Testosterone supplementation is effective in the short-term. However, its long-term safety is unclear.

Surgery is sometimes performed to alter the appearance of the genitals. However many surgeries performed on intersex people lack clear evidence of necessity, can be considered as mutilating, and are widely considered to be human rights violations when performed without the informed consent of the recipient.

Testosterone has been used to successfully treat undervirilization in some but not all men with PAIS, despite having supraphysiological levels of testosterone to start with. Treatment options include transdermal gels or patches, oral or injectable testosterone undecanoate, other injectable testosterone esters, testosterone pellets, or buccal testosterone systems. Supraphysiological doses may be required to achieve the desired physiological effect, which may be difficult to achieve using non-injectable testosterone preparations. Exogenous testosterone supplementation in unaffected men can produce various unwanted side effects, including prostatic hypertrophy, polycythemia, gynecomastia, hair loss, acne, and the suppression of the hypothalamic-pituitary-gonadal axis, resulting in the reduction of gonadotropins (i.e., luteinizing hormone and follicle-stimulating hormone) and spermatogenic defect. These effects may not manifest at all in men with AIS, or might only manifest at a much higher concentration of testosterone, depending on the degree of androgen insensitivity. Those undergoing high dose androgen therapy should be monitored for safety and efficacy of treatment, possibly including regular breast and prostate examinations. Some individuals with PAIS have a sufficiently high sperm count to father children; at least one case report has been published that describes fertile men who fit the criteria for grade 2 PAIS (micropenis, penile hypospadias, and gynecomastia). Several publications have indicated that testosterone treatment can correct low sperm counts in men with MAIS. At least one case report has been published that documents the efficacy of treating a low sperm-count with tamoxifen in an individual with PAIS.

Some have hypothesized that supraphysiological levels of estrogen may reduce the diminished bone mineral density associated with CAIS. Data has been published that suggests affected women who were not compliant with estrogen replacement therapy, or who had a lapse in estrogen replacement, experienced a more significant loss of bone mineral density. Progestin replacement therapy is seldom initiated, due to the absence of a uterus. Androgen replacement has been reported to increase a sense of well-being in gonadectomized women with CAIS, although the mechanism by which this benefit is achieved is not well understood.

XX males are sterile due to low or no sperm content and there is currently no treatment to address this infertility. Genital ambiguities, while not necessary to treat for medical reasons, can be treated through the use of hormonal therapy, surgery, or both. Since XX male syndrome is variable in its presentation, the specifics of treatment varies widely as well. In some cases gonadal surgery can be performed to remove partial or whole female genitalia. This may be followed by plastic and reconstructive surgery to make the individual appear more externally male. Conversely, the individual may wish to become more feminine and feminizing genitoplasty can be performed to make the ambiguous genitalia appear more female. Hormonal therapy may also aid in making an individual appear more male or female.

Genitoplasty, unlike gender assignment, can be irreversible, and there is no guarantee that adult gender identity will develop as assigned despite surgical intervention. Some aspects of genitoplasty are still being debated; a variety of different opinions have been presented by professionals, self-help groups, and patients over the last few decades. Points of consideration include what conditions justify genitoplasty, the extent and type of genitoplasty that should be employed, when genitoplasty should be performed, and what the goals of genitoplasty should be. Gender assignment itself does not predicate the need for immediate genitoplasty; in some cases, surgical intervention can be delayed to allow the affected child to reach an age and maturity sufficient to have a role in such decisions. Some studies suggest that early surgeries can still produce satisfactory outcomes, while others suggest it to be unlikely. Even surgeries that are planned as one-stage procedures often require further major surgery. Scarring and tissue loss that result from repeated surgical procedures are of particular concern, due to the presumed negative impact on sexual function.

While it is thought that feminizing genitoplasty typically requires fewer surgeries to achieve an acceptable result and results in fewer urologic difficulties, there is no evidence that feminizing surgery results in a better psychosocial outcome. In one study, individuals with grade 3 PAIS who were raised male rated their body image and sexual function similarly to those who were raised female, even though they were more likely to have genitalia that were abnormal in size and appearance; more than half of the male participants had a stretched penile length that was below 2.5 standard deviations of the mean, while only 6% of female participants presented with a short vagina in adulthood, and participating physicians gave a lower cosmetic rating to the surgical results of the men than the women. Both male and female participants cited the appearance of their genitalia as being the greatest contributing factor to their dissatisfaction with their body image. In two larger studies, the common predictor of gender reassignment was stigmatization related to having an intersex condition.

The outcome of masculinizing genitoplasty is dependent on the amount of erectile tissue and the extent of hypospadias. Procedures include correction of penile curvature and chordee, reconstruction of the urethra, hypospadias correction, orchidopexy, and Müllerian remnant removal to prevent infection and pseudo-incontinence. Erectile prosthesis may be inserted in cases of successful neophalloplasty in adulthood, although it has a high morbidity. Additional surgeries may be required to correct postsurgical complications such as stenosis of the anastomosis between the native urethra and the graft, urethral fistulas, and posterior displacement of the balanic meatus. Successful masculinizing genitoplasty performed on individuals with grade 3 PAIS often requires multiple surgeries.

If feminizing genitoplasty is performed in infancy, the result will need to be refined at puberty through additional surgery. Procedures include clitoral reduction / recession, labiaplasty, repair of the common urogenital sinus, vaginoplasty, and vaginal dilation through non-surgical pressure methods. Clitoral reduction / recession surgery carries with it the risk of necrosis as well as the risk of impairing the sexual function of the genitalia, and thus should not be performed for less severe clitoromegaly. Clitoral surgery should be focused on function rather than appearance, with care being taken to spare the erectile function and innervation of the clitoris. If PAIS presents with a common urogenital sinus, the American Academy of Pediatrics currently recommends that surgery to separate the urethra from the vagina be performed at an early age. As is the case for CAIS, vaginal dilation using pressure dilation methods should be attempted before the surgical creation of a neovagina is considered, and neither should be performed before puberty. Complications of feminizing genitoplasty can include vaginal stenosis, meatal stenosis, vaginourethral fistula, female hypospadias, urinary tract injuries, and recurrent clitoromegaly. Successful feminizing genitoplasty performed on individuals with grade 3 PAIS often requires multiple surgeries, although more surgeries are typically required for successful masculinizing genitoplasty in this population.

Many surgical procedures have been developed to create a neovagina, as none of them is ideal. Surgical intervention should be considered only after non-surgical pressure dilation methods have failed to produce a satisfactory result. Neovaginoplasty can be performed using skin grafts, a segment of bowel, ileum, peritoneum, , buccal mucosa, amnion, or dura mater. Success of such methods should be determined by sexual function, and not by vaginal length alone, as has been done in the past. Ileal or cecal segments may be problematic because of a shorter mesentery, which may produce tension on the neovagina, leading to stenosis. The sigmoid neovagina is thought to be self-lubricating, without the excess mucus production associated with segments of small bowel. Vaginoplasty may create scarring at the introitus (the vaginal opening), requiring additional surgery to correct. Vaginal dilators are required postoperatively to prevent vaginal stenosis from scarring. Other complications include bladder and bowel injuries. Yearly exams are required, as neovaginoplasty carries a risk of carcinoma, although carcinoma of the neovagina is uncommon. Neither neovaginoplasty nor vaginal dilation should be performed before puberty.

A problem for people with penile agenesis is the absence of a urinary outlet. Before genital metamorphosis, the urethra runs down the anal wall, to be pulled away by the genital tubercle during male development. Without male development this does not occur. The urethra can be surgically redirected to the rim of the anus immediately after birth to enable urination and avoid consequent internal irritation from urea concentrate. In such cases, the perineum may be left devoid of any genitalia, male or female.

A working penis transplant on to an agenetic patient has never been successful. Only one major penis graft was successfully completed. This occurred in China and the patient shortly rejected it on psychological grounds. However a full female or agenetic to male transplant is not yet facilitated to fulfil full reproductive functions.

On March 18, 2013, it was announced that Andrew Wardle, a British man born without a penis, was going to receive a pioneering surgery to create a penis for him. The surgeons hope to "fold a large flap of skin from his arm — complete with its blood vessels and nerves — into a tube to graft onto his pubic area." If the surgery goes well, the odds of starting a family are very good.

Surgery (orchiopexy) to retrieve the testes and position them in the scrotum is the primary treatment. Occasionally they are unsalvageable if located high in the retroperitoneum. During this surgery, the uterus is usually removed and attempts made to dissect away Müllerian tissue from the vas deferens and epididymis to improve the chance of fertility. If the person has male gender identity himself and the testes cannot be retrieved, testosterone replacement will be usually necessary at puberty should the affected individual choose to pursue medical attention. Lately, laparoscopic hysterectomy is offered to patients as a solution to both improve the chances of fertility and to prevent the occurrences of neoplastic tissue formation.

Due to its mild presentation, MAIS often goes unnoticed and untreated. Management of MAIS is currently limited to symptomatic management; methods to correct a malfunctioning androgen receptor protein that result from an AR gene mutation are not currently available. Treatment includes surgical correction of mild gynecomastia, minor hypospadias repair, and testosterone supplementation. Supraphysiological doses of testosterone have been shown to correct diminished secondary sexual characteristics in men with MAIS, as well as to reverse infertility due to low sperm count. As is the case with PAIS, men with MAIS will experience side effects from androgen therapy (such as the suppression of the hypothalamic-pituitary-gonadal axis) at a higher dosage than unaffected men. Careful monitoring is required to ensure the safety and efficacy of treatment. Regular breast and prostate examinations may be necessary due to comorbid association with breast and prostate cancers.

The FDA has approved one medication for the treatment of disorders of female libido, flibanserin.

Biological treatments physically alter primary and secondary sex characteristics to reduce the discrepancy between an individual's physical body and gender identity. Biological treatments for GID without any form of psychotherapy is quite uncommon. Researchers have found that if individuals bypass psychotherapy in their GID treatment, they often feel lost and confused when their biological treatments are complete.

Psychotherapy, hormone replacement therapy, and sex reassignment surgery together can be effective treating GID when the WPATH standards of care are followed. The overall level of patient satisfaction with both psychological and biological treatments is very high.

Selective serotonin reuptake inhibitors (SSRIs) are used, especially with exhibitionists, non-offending pedophiles, and compulsive masturbators. They are proposed to work by reducing sexual arousal, compulsivity, and depressive symptoms. However, supporting evidence for SSRIs is limited.

Antiandrogens are used in more severe cases. Similar to physical castration, they work by reducing androgen levels, and have thus been described as chemical castration. The antiandrogen cyproterone acetate has been shown to substantially reduce sexual fantasies and offending behaviors. Medroxyprogesterone acetate and gonadotropin-releasing hormone agonists (such as leuprolide acetate) have also been used to lower sex drive. Due to the side effects, the World Federation of Societies of Biological Psychiatry recommends that hormonal treatments only be used when there is a serious risk of sexual violence, or when other methods have failed. Surgical castration has largely been abandoned because these pharmacological alternatives are similarly effective and less invasive.

The uterine curettage is generally done under the effect of anesthesia, preferably spinal anesthesia in hemodynamically stable patients. The advantages of spinal anesthesia over general anesthesia include ease of technique, favorable effects on the pulmonary system, safety in patients with hyperthyroidism and non-tocolytic pharmacological properties. Additionally, by maintaining patient’s consciousness one can diagnose the complications like uterine perforation, cardiopulmonary distress and thyroid storm at an earlier stage than when the patient is sedated or is under general anesthesia.

Until the 1970s, psychotherapy was the primary treatment for gender dysphoria, and generally was directed to helping the person adjust to the gender of the physical characteristics present at birth. Psychotherapy is any therapeutic interaction that aims to treat a psychological problem. Though some clinicians still use only psychotherapy to treat gender dysphoria, it may now be used in addition to biological interventions. Psychotherapeutic treatment of GID involves helping the patient to adapt. Attempts to cure GID by changing the patient's gender identity to reflect birth characteristics have been ineffective.

According to the World Health Organization, fetishistic fantasies are common and should only be treated as a disorder when they impair normal functioning or cause distress. Goals of treatment can include elimination of criminal activity, reduction in reliance on the fetish for sexual satisfaction, improving relationship skills, or attempting to remove deviant arousal altogether. The evidence for treatment efficacy is limited and largely based on case studies, and no research on treatment for female fetishists exists.

Cognitive behavioral therapy is one popular approach. Cognitive behavioral therapists teach clients to identify and avoid antecedents to fetishistic behavior, and substitute non-fetishistic fantasies for ones involving the fetish. Aversion therapy can reduce fetishistic arousal in the short term, but is unlikely to have any permanent effect.

Antiandrogens and selective serotonin reuptake inhibitors (SSRIs) may be prescribed to lower sex drive. Cyproterone acetate is the most commonly used antiandrogen, except in the United States, where it may not be available. A large body of literature has shown that it reduces general sexual fantasies. Side effects may include osteoporosis, liver dysfunction, and feminization. Case studies have found that the antiandrogen medroxyprogesterone acetate is successful in reducing sexual interest, but can have side effects including osteoporosis, diabetes, deep vein thrombosis, feminization, and weight gain. Some hospitals use leuprolide acetate and goserelin acetate to reduce libido, and while there is presently little evidence for their efficacy, they have fewer side effects than other antiandrogens. A number of studies support the use of SSRIs, which may be preferable over antiandrogens because of their relatively benign side effects. None of these drugs cure sexual fetishism, but they can make it easier to manage.

Relationship counselers may attempt to reduce dependence on the fetish and improve partner communication using techniques like sensate focusing. Partners may agree to incorporate the fetish into their activities in a controlled, time-limited manner, or set aside only certain days to practice the fetishism. If the fetishist cannot sustain an erection without the fetish object, the therapist might recommend orgasmic reconditioning or covert sensitization to increase arousal to normal stimuli (although the evidence base for these techniques is weak).

Hydatidiform moles should be treated by evacuating the uterus by uterine suction or by surgical curettage as soon as possible after diagnosis, in order to avoid the risks of choriocarcinoma. Patients are followed up until their serum human chorionic gonadotrophin (hCG) level has fallen to an undetectable level. Invasive or metastatic moles (cancer) may require chemotherapy and often respond well to methotrexate. As they contain paternal antigens, the response to treatment is nearly 100%. Patients are advised not to conceive for half a year after hCG levels have normalized. The chances of having another molar pregnancy are approximately 1%.

Management is more complicated when the mole occurs together with one or more normal fetuses.

Patients with Leydig cell hypoplasia may be treated with hormone replacement therapy (i.e., with androgens), which will result in normal sexual development and the resolution of most symptoms. In the case of 46,XY (genetically "male") individuals who are phenotypically female and/or identify as the female gender, estrogens should be given instead. Surgical correction of the genitals in 46,XY males may be required, and, if necessary, an orchidopexy (relocation of the undescended testes to the scrotum) may be performed as well.

Management of AIS is currently limited to symptomatic management; no method is currently available to correct the malfunctioning androgen receptor proteins produced by "AR" gene mutations. Areas of management include sex assignment, genitoplasty, gonadectomy in relation to tumor risk, hormone replacement therapy, genetic counseling, and psychological counseling.

Treatment depends on diagnosis and may include hormonal therapy, iv fluids, blood transfusion, and/or a dilation and curettage. Internal bleeding requires laparoscopy or abdominal surgery, in rare and extreme cases a hysterectomy is performed.

Upon diagnosis, estrogen and progesterone therapy is typically commenced, promoting the development of female characteristics.

The consequences of streak gonads to a person with Swyer syndrome:

1. Gonads cannot make estrogen, so the breasts will not develop and the uterus will not grow and menstruate until estrogen is administered. This is often given transdermally.

2. Gonads cannot make progesterone, so menstrual periods will not be predictable until progestin is administered, usually as a pill.

3. Gonads cannot produce eggs so conceiving children naturally is not possible. A woman with a uterus and ovaries but without female gamete is able to become pregnant by implantation of another woman's fertilized egg (embryo transfer).

4. Streak gonads with Y chromosome-containing cells have a high likelihood of developing cancer, especially gonadoblastoma. Streak gonads are usually removed within a year or so of diagnosis since the cancer can begin during infancy.

Males and females may be treated with hormone replacement therapy (i.e., with androgens and estrogens, respectively), which will result in normal sexual development and resolve most symptoms. In the case of 46,XY (genetically male) individuals who are phenotypically female and/or identify as the female gender, they should be treated with estrogens instead. Removal of the undescended testes should be performed in 46,XY females to prevent their malignant degeneration, whereas in 46,XY males surgical correction of the genitals is generally required, and, if necessary, an orchidopexy (relocation of the undescended testes to the scrotum) may be performed as well. Namely in genetic females presenting with ovarian cysts, GnRH analogues may be used to control high FSH and LH levels if they are unresponsive to estrogens.

Pharmacological interventions are used to lower the sex drive in general, which can ease the management of pedophilic feelings, but does not change sexual preference. Antiandrogens work by interfering with the activity of testosterone. Cyproterone acetate (Androcur) and medroxyprogesterone acetate (Depo-Provera) are the most commonly used. The efficacy of antiantrogens has some support, but few high-quality studies exist. Cyproterone acetate has the strongest evidence for reducing sexual arousal, while findings on medroxyprogesterone acetate have been mixed.

Gonadotropin-releasing hormone analogues such as leuprolide acetate (Lupron), which last longer and have fewer side-effects, are also used to reduce libido, as are selective serotonin reuptake inhibitors. The evidence for these alternatives is more limited and mostly based on open trials and case studies. All of these treatments, commonly referred to as "chemical castration", are often used in conjunction with cognitive behavioral therapy. According to the Association for the Treatment of Sexual Abusers, when treating child molesters, "anti-androgen treatment should be coupled with appropriate monitoring and counseling within a comprehensive treatment plan." These drugs may have side-effects, such as weight gain, breast development, liver damage and osteoporosis.

Historically, surgical castration was used to lower sex drive by reducing testosterone. The emergence of pharmacological methods of adjusting testosterone has made it largely obsolete, because they are similarly effective and less invasive. It is still occasionally performed in Germany, the Czech Republic, Switzerland, and a few U.S. states. Non-randomized studies have reported that surgical castration reduces recidivism in contact sex offenders. The Association for the Treatment of Sexual Abusers opposes surgical castration and the Council of Europe works to bring the practice to an end in Eastern European countries where it is still applied through the courts.