Links between maternal smoking and TDS are tenuous, but there are stronger associations between maternal alcohol consumption and incidences of cryptorchidism in sons. Smoking does however affect the growth of a fetus, and low birth weight is shown to increase the likelihood of all the disorders encompassed by TDS. Maternal obesity, resulting in gestational diabetes, has also been shown to be a risk factor for impaired testes development and TDS symptoms in sons.

It is a rare condition, with only approximately 60 cases reported as of 1989, and 75 cases as of 2005. However, due to the stigma of intersex conditions and the issues of keeping accurate statistics and records among doctors, it is likely there are more cases than reported.

It is also known that disruption of the endocrine system by certain chemicals adversely affects the development of the reproductive system and can cause vaginal cancer. Many other reproductive diseases have also been link to exposure to synthetic and environmental chemicals. Common chemicals with known links to reproductive disorders include: lead, dioxins and dioxin-like compounds, styrene, toluene, BPA (Bisphenol A) and pesticides.

Exposure of a male fetus to substances that disrupt hormone systems, particularly chemicals that inhibit the action of androgens (male sex hormones) during the development of the reproductive system, has been shown to cause many of the characteristic TDS disorders. These include environmental estrogens and anti-androgens found in food and water sources that have been contaminated with synthetic hormones and pesticides used in agriculture. In historical cases, medicines given to pregnant women, like diethylstilbestrol (DES), have caused many of the features of TDS in fetuses exposed to this chemical during gestation. The impact of environmental chemicals is well documented in animal models. If a substance affects Sertoli and Leydig cell differentiation (a common feature of TDS disorders) at an early developmental stage, germ cell growth and testosterone production will be impaired. These processes are essential for testes descent and genitalia development, meaning that genital abnormalities like cryptorchidism or hypospadias may be present from birth, and fertility problems and TGCC become apparent during adult life. Severity or number of disorders may therefore be dependent on the timing of the environmental exposure. Environmental factors can act directly, or via epigenetic mechanisms, and it is likely that a genetic susceptibility augmented by environmental factors is the primary cause of TDS.

Even with successful surgery, patients may have long-term problems with:

- incontinence, where serious usually treated with some form of continent urinary diversion such as the Mitrofanoff

- depression and psycho-social complications

- sexual dysfunction

Surgical intervention for a number of conditions may remove anatomical structures necessary to erection, damage nerves, or impair blood supply. Erectile dysfunction is a common complication of treatments for prostate cancer, including prostatectomy and destruction of the prostate by external beam radiation, although the prostate gland itself is not necessary to achieve an erection. As far as inguinal hernia surgery is concerned, in most cases, and in the absence of postoperative complications, the operative repair can lead to a recovery of the sexual life of patients with preoperative sexual dysfunction, while, in most cases, it does not affect patients with a preoperative normal sexual life.

ED can also be associated with bicycling due to both neurological and vascular problems due to compression. The increase risk appears to be about 1.7-fold.

Concerns that use of pornography can cause erectile dysfunction have not been substantiated in epidemiological studies according to a recent literature review. However, another review and case studies article maintains that use of pornography does indeed cause erectile dysfunction, and critiques the previously described literature review.

Examples of congenital abnormalities of the reproductive system include:

- Kallmann syndrome - Genetic disorder causing decreased functioning of the sex hormone-producing glands caused by a deficiency or both testes from the scrotum.

- Androgen insensitivity syndrome - A genetic disorder causing people who are genetically male (i.e. XY chromosome pair) to develop sexually as a female due to an inability to utilize androgen.

- Intersexuality - A person who has genitalia and/or other sexual traits which are not clearly male or female.

The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.

Aphallia has no known cause. It is not linked to deficient hormone amounts or action, but rather to a failure of the fetal genital tubercle to form between 3 and 6 weeks after conception. The urethra of an affected child opens on the perineum.

Erectile dysfunction is characterized by the regular or repeated inability to obtain or maintain an erection.

Anejaculation is the pathological inability to ejaculate in males, with ("orgasmic") or without ("anorgasmic") orgasm.

In an embryo, the conversion of the gonads into testicles in males-to-be and into ovaries in females-to-be is the function of Leydig cells. In testicular agenesis, this process fails. Penile agenesis can be caused by testicular agenesis. Testes are the sole producer of 5-alpha dihydrotestosterone (5aDHT) in the male body. Where the gonads fail to metamorphose into testes, there is no 5aDHT. Therefore, the masculising process that builds the genital tubercle, the precursor to the penis, is stillborn. When this happens, the child is born with both penile and testicular agenesis and is known by the slang term "nullo". This combination of both conditions is estimated to occur in between 20-30 million male births.

Penile agenesis can exist independently after full testicular development; in this case its cause is unknown.

The numbers of women with SCI giving birth and having healthy babies are increasing. Around a half to two-thirds of women with SCI report they might want to have children, and 14–20% do get pregnant at least once. Although female fertility is not usually permanently reduced by SCI, there is a stress response that can happen immediately post-injury that alters levels of fertility-related hormones in the body. In about half of women, menstruation stops after the injury but then returns within an average of five months—it returns within a year for a large majority. After menstruation returns, women with SCI become pregnant at a rate close to that of the rest of the population.

Pregnancy is associated with greater-than-normal risks in women with SCI, among them increased risk of deep vein thrombosis, respiratory infection, and urinary tract infection. Considerations exist such as maintaining proper positioning in a wheelchair, prevention of pressure sores, and increased difficulty moving due to weight gain and changes in center of balance. Assistive devices may need to be altered and medications changed.

For women with injuries above T6, a risk during labor and delivery that threatens both mother and fetus is autonomic dysreflexia, in which the blood pressure increases to dangerous levels high enough to cause potentially deadly stroke. Drugs such as nifedipine and captopril can be used to manage an episode if it occurs, and epidural anesthesia helps although it is not very reliable in women with SCI. Anesthesia is used for labor and delivery even for women without sensation, who may only experience contractions as abdominal discomfort, increased spasticity, and episodes of autonomic dysreflexia. Reduced sensation in the pelvic area means women with SCI usually have less painful delivery; in fact, they may fail to realize when they go into labor. If there are deformities in the pelvis or spine caesarian section may be necessary. Babies of women with SCI are more likely to be born prematurely, and, premature or not, they are more likely to be small for their gestational time.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

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.

Penile fracture is a relatively uncommon clinical condition. Vaginal intercourse and aggressive masturbation are the most common causes. A 2014 study of accident and emergency records at three hospitals in Campinas, Brazil, showed that woman on top positions caused the greatest risk with the missionary position being the safest. The research conjectured that when a woman is on top, she usually controls the movement and her entire body weight lands on the erect penis. She is not able to interrupt movement when the penis suffers a misaligned penetration. Conversely, when the man is controlling the movement, he has better chances of stopping the penetration thrusts in response to pain, minimizing harm to himself.

The practice of "taqaandan" (also "taghaandan") also puts men at risk of penile fracture. Taqaandan, which comes from a Kurdish word meaning "to click", involves bending the top part of the erect penis while holding the lower part of the shaft in place, until a click is heard and felt. Taqaandan is said to be painless and has been compared to cracking one's knuckles, but the practice of taqaandan has led to an increase in the prevalence of penile fractures in western Iran. Taqaandan may be performed to achieve detumescence.

Gonadectomy at time of diagnosis is the current recommendation for PAIS if presenting with cryptorchidism, due to the high (50%) risk of germ cell malignancy. The risk of malignancy when testes are located intrascrotally is unknown; the current recommendation is to biopsy the testes at puberty, allowing investigation of at least 30 seminiferous tubules, with diagnosis preferably based on OCT3/4 immunohistochemistry, followed by regular examinations. Hormone replacement therapy is required after gonadectomy, and should be modulated over time to replicate the hormone levels naturally present in the body during the various stages of puberty. Artificially induced puberty results in the same, normal development of secondary sexual characteristics, growth spurt, and bone mineral accumulation. Women with PAIS may have a tendency towards bone mineralization deficiency, although this increase is thought to be less than is typically seen in CAIS, and is similarly managed.

It can depend on one or more of several causes, including:

- Sexual inhibition

- Pharmacological inhibition. They include mostly antidepressant and antipsychotic medication, and the patients experiencing that tend to quit them

- Autonomic nervous system

- Prostatectomy - surgical removal of the prostate.

- Ejaculatory duct obstruction

- Spinal cord injury causes sexual dysfunction including anejaculation. The rate of being able to ejaculate varies with the type of lesion, as detailed in the table at right.

- old age

Anejaculation, especially the "orgasmic" variant, is usually indistinguishable from retrograde ejaculation. However, a negative urinalysis measuring no abnormal presence of spermatozoa in the urine will eliminate a retrograde ejaculation diagnosis.

Thus, if the affected man has the sensations and involuntary muscle-contractions of an orgasm but no or very low-volume semen, ejaculatory duct obstruction is another possible underlying pathology of anejaculation.

A bifid penis (or double penis) is a rare congenital defect where two genital tubercles develop.

Historically, males born with a bifid penis often underwent sex reassignment surgery, due to the difficulty of penile reconstruction. They were raised as girls, and often had reconstructive surgery to make them phenotypically female, coupled with female hormone replacement therapy. However, in recent years, this practice has fallen under heavy scrutiny due to both a high frequency of sexual dysfunction in gender converted children, and more advanced penile reconstruction techniques.

Many male marsupials naturally have a bifid penis, with left and right prongs that they insert into multiple vaginal canals simultaneously.

Men with SCI rank the ability to father children among their highest concerns relating to sexuality. Male fertility is reduced after SCI, due to a combination of problems with erections, ejaculation, and quality of the semen. As with other types of sexual response, ejaculation can be psychogenic or reflexogenic, and the level of injury affects a man's ability to experience each type. As many as 95% of men with SCI have problems with ejaculation (anejaculation), possibly due to impaired coordination of input from different parts of the nervous system. Erection, orgasm, and ejaculation can each occur independently, although the ability to ejaculate seems linked to the quality of the erection, and the ability to orgasm is linked to the ejaculation facility. Even men with complete injuries may be able to ejaculate, because other nerves involved in ejaculation can effect the response without input from the spinal cord. In general, the higher the level of injury, the more physical stimulation the man needs to ejaculate. Conversely, premature or spontaneous ejaculation can be a problem for men with injuries at levels T12–L1. It can be severe enough that ejaculation is provoked by thinking a sexual thought, or for no reason at all, and is not accompanied by orgasm.

Most men have a normal sperm count, but a high proportion of sperm are abnormal; they are less motile and do not survive as well. The reason for these abnormalities is not known, but research points to dysfunction of the seminal vesicles and prostate, which concentrate substances that are toxic to sperm. Cytokines, immune proteins which promote an inflammatory response, are present at higher concentrations in semen of men with SCI, as is platelet-activating factor acetylhydrolase; both are harmful to sperm. Another immune-related response to SCI is the presence of a higher number of white blood cells in the semen.

Penetrating and blunt traumas combined make up approximately 90% of all civilian penile injuries (45% each), with burns and other accidents making up the remaining 10%.

The causes of penile injury are mostly the same as other causes of trauma; however, penile injury is more likely to occur during sexual intercourse and masturbation than other traumas. Nocturnal erections and sleeping positions can be another cause of penile injury. Industrial and automobile accidents can also cause penile injury. Self-injury may also affect the penis.

The causes of premature ejaculation are unclear. Many theories have been suggested, including that PE was the result of masturbating quickly during adolescence to avoid being caught, of performance anxiety, of an unresolved Oedipal conflict, of passive-aggressiveness, and having too little sex; but there is little evidence to support any of these theories.

Several physiological mechanisms have been hypothesized to contribute to causing premature ejaculation including serotonin receptors, a genetic predisposition, elevated penile sensitivity, and nerve conduction atypicalities.

The nucleus paragigantocellularis of the brain has been identified as having involvement in ejaculatory control. Scientists have long suspected a genetic link to certain forms of premature ejaculation. In one study, 91 percent of men who have had premature ejaculation for their entire lives also had a first-relative with lifelong premature ejaculation. Other researchers have noted that men who have premature ejaculation have a faster neurological response in the pelvic muscles.

PE may be caused by prostatitis or as a drug side effect.

Webbed penis, also called penis palmatus or penoscrotal fusion, is an acquired or congenital condition in which the scrotal skin extends onto the ventral penile shaft. The penile shaft is buried in scrotum or tethered to the scrotal midline by a fold or web of skin. The urethra and erectile bodies are usually normal. Webbed penis is usually asymptomatic, but the cosmetic appearance is often unacceptable. This condition may be corrected by surgical techniques.

In the congenital form, the deformity represents an abnormality of the attachment between the penis and the scrotum; the penis, the urethra, and the remainder of the scrotum typically are normal.

Webbed penis may also be acquired (iatrogenic) after circumcision or other penile surgery, resulting from excessive removal of ventral penile skin; the penis can retract into the scrotum, resulting in secondary phimosis (trapped penis).

One procedure for webbed penis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

Paraphimosis can be avoided by bringing the foreskin back into its normal, forward, non-retracted position after retraction is no longer necessary (for instance, after cleaning the glans penis or placing a Foley catheter). Phimosis (both pathologic and normal childhood physiologic forms) is a risk factor for paraphimosis; "physiologic" phimosis resolves naturally as a child matures, but it may be advisable to treat "pathologic" phimosis via long-term stretching or elective surgical techniques (such as preputioplasty to loosen the preputial orifice or circumcision to amputate the foreskin tissue partially or completely).

The foreskin responds to the application of tension to cause expansion by creating new skin cells though the process of mitosis. The tissue expansion is permanent. Non-surgical stretching of the foreskin may be used to widen a narrow, non-retractable foreskin. Stretching may be combined with the use of a steroid cream. Beaugé recommends manual stretching for young males in preference to circumcision as a treatment for non-retractile foreskin because of the preservation of sexual sensation.

Paraphimosis can often be effectively treated by manual manipulation of the swollen foreskin tissue. This involves compressing the glans and moving the foreskin back to its normal position, perhaps with the aid of a lubricant, cold compression, and local anesthesia as necessary. If this fails, the tight edematous band of tissue can be relieved surgically with a dorsal slit or circumcision. An alternative method, the Dundee technique, entails placing multiple punctures in the swollen foreskin with a fine needle, and then expressing the edema fluid by manual pressure. According to Ghory and Sharma, treatment by circumcision may be elected as "a last resort, to be performed by a urologist". Other experts recommend delaying elective circumcision until after paraphimosis has been resolved.