Hypospadias presents as an abnormal location for the end of the urethra which is typically found on the distal end of the penis. It is generally diagnosed at birth from visual confirmation of the hallmark features. As well as an unusual location of the urethra, the prepuce (foreskin) is typically incomplete as well. The abnormal ‘hooded’ prepuce is what often draws attention to the condition but can occur separately to hypospadias.

In Cryptorchidism a diagnosis is made from a physical examination which is performed when the baby is lacking one or both testes in the dependant portion of the scrotal sac. 70% of cryptorchid testes can be felt and are unable to be pulled into the scrotum or retreats quickly after being pulled into a higher position. In 30% of cases the testes cannot be felt indicating an intra-abdominal location. The risk factors for Cryptorchidism are:

- A family history of the condition

- Low birth weight

- Prematurity

PPSH usually consists of:

- a phallus midway in size between penis and clitoris,

- a chordee tethering it to the perineum,

- a urethral opening usually on the perineum (the hypospadias),

- and an incompletely closed urogenital opening, which resembles a small and shallow vagina.

Testes are often palpable in the scrotum or inguinal canals, and the karyotype is XY. In most cases there are no internal female structures such as a uterus or other Müllerian duct derivatives.

It is considered a form of 5-alpha-reductase deficiency involving SRD5A2.

Because both the Wolffian ducts and Müllerian ducts begin to develop, the tissues are often intertwined, resulting in obstruction or nonpatency of the vas deferens or other parts of the reproductive excretory ducts. This can result in infertility, the most serious potential problem caused by this condition. Sometimes, transverse testicular ectopia is evident.

Cryptorchidism in AMH deficiency suggests that AMH may play a role in transabdominal testicular descent, perhaps by facilitating contraction of the gubernaculum.

Other Müllerian derivatives which may be present in at least a rudimentary form are the cervix, upper part of the vagina, and fallopian tubes.

The condition can come to attention because of a bulge in the inguinal canal of an XY infant due to herniation of the uterus. The presence of a uterus may be noticed if an ultrasound or MRI of the pelvis is performed to locate the testes or for other reasons. Occasionally the uterus is discovered during abdominal surgery for some other purpose in later childhood or adult life.

Although persistent Müllerian duct syndrome is classified as an intersex condition, it does not involve ambiguity or malformation of the external genitalia, which appear typical (apart from cryptorchidism if present). Sometimes the uterus enters a hernia. Sometimes the Müllerian structures get entangled with the spermatic ducts and interfere with the descent of the testes.

Apart from humans, this syndrome has been reported in dogs.

Persistent Müllerian duct syndrome (PMDS) is the presence of Müllerian duct derivatives (fallopian tubes, uterus, and/or the upper part of the vagina) in what would be considered a genetically and otherwise physically normal male animal by typical human based standards. In humans, PMDS typically is due to an autosomal recessive congenital disorder and is considered by some to be a form of pseudohermaphroditism due to the presence of Müllerian derivatives.

Typical features include undescended testes (cryptorchidism) and the presence of a small, underdeveloped uterus in an XY infant or adult. This condition is usually caused by deficiency of fetal anti-Müllerian hormone (AMH) effect due to mutations of the gene for AMH or the anti-Müllerian hormone receptor, but may also be as a result of insensitivity to AMH of the target organ.

Testicular torsion usually presents with sudden, severe, testicular pain (in groin and lower abdomen) and tenderness. There is often associated nausea and vomiting. The testis may be higher than its normal position. Mild pyrexia and redness of overlying area may be found.

Some of the symptoms are similar to epididymitis though epididymitis may be characterized by discoloration and swelling of the testis, often with fever, while the cremasteric reflex is usually present. Testicular torsion, or more probably impending testicular infarction, can also produce a low-grade fever.

There is often an absent or decreased cremasteric reflex.

Cryptorchidism is the absence of one or both testes from the scrotum. It is the most common birth defect of the male genital. About 3% of full-term and 30% of premature infant boys are born with at least one undescended testis. However, about 80% of cryptorchid testes descend by the first year of life (the majority within three months), making the true incidence of cryptorchidism around 1% overall. Cryptorchidism may develop after infancy, sometimes as late as young adulthood, but that is exceptional.

Cryptorchidism is distinct from monorchism, the condition of having only one testicle. The condition may occur on one or both sides; it more commonly affects the right testis.

A testis absent from the normal scrotal position may be:

1. anywhere along the "path of descent" from high in the posterior (retroperitoneal) abdomen, just below the kidney, to the inguinal ring;

2. in the inguinal canal;

3. "ectopic", having "wandered" from the path of descent, usually outside the inguinal canal and sometimes even under the skin of the thigh, the perineum, the opposite scrotum, or the femoral canal;

4. undeveloped ("hypoplastic") or severely abnormal ("dysgenetic");

5. missing (also see anorchia).

About two-thirds of cases without other abnormalities are unilateral; most of the other third involve both testes. In 90% of cases an undescended testis can be felt in the inguinal canal. In a small minority of cases missing testes may be found in the abdomen or appear to be nonexistent (truly "hidden").

Undescended testes are associated with reduced fertility, increased risk of testicular germ cell tumors and psychological problems when the boy is grown. Undescended testes are also more susceptible to testicular torsion (and subsequent infarction) and inguinal hernias. Without intervention, an undescended testicle will usually descend during the first year of life, but to reduce these risks, undescended testes can be brought into the scrotum in infancy by a surgical procedure called an orchiopexy.

Although cryptorchidism nearly always refers to "congenital" absence or maldescent, a testis observed in the scrotum in early infancy can occasionally "reascend" (move back up) into the inguinal canal. A testis which can readily move or be moved between the scrotum and canal is referred to as "retractile". The word is from the Greek "κρυπτός", "kryptos", meaning hidden "ὄρχις", "orchis", meaning testicle.

Cryptorchidism, hypospadias, testicular cancer and poor semen quality make up the syndrome known as testicular dysgenesis syndrome.

Aphallia is a congenital malformation in which the phallus (penis or clitoris) is absent. It is the female counterpart of penile agenesis and testicular agenesis. The word is derived from the Greek "a-" for "not", and "phallos" for "penis". It is classified as an intersex condition.

Males with penile agenesis but normal testes are of otherwise normal male appearance.

Males with testicular agenesis tend not to produce the reproductive hormone 5aDHT at any stage of their lives. As a result, they tend toward prepubescent appearance, with infantile skin texture, developing little body hair particularly in the crotch area, even vellus hair. Without genitalia of either sex, the perineum is therefore left smooth. Also muscular development is retarded and testicular agenetics are of rather frail build with short limbs and small hands and feet.

However certain male features are results of other male gender-marker hormones, "androgens", which develop male secondary sex characteristics, among which features are the deepening of the voice and facial hair.

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.

Microorchidism is a genetic disorder found in males, characterized by abnormally small testes. The condition is associated with (and often secondary to) a number of other genetic disorders, including Klinefelter's Syndrome and Prader-Willi syndrome, as well as other multiple malformation disorders. The degree of abnormality (or otherwise) of the testes can be determined by the use of an orchidometer. In addition, Microorchidism may also occur as a result of shrinkage or atrophy of the testis due to infections like mumps.

Many men who were born with undescended testes have reduced fertility, even after orchiopexy in infancy. The reduction with unilateral cryptorchidism is subtle, with a reported infertility rate of about 10%, compared with about 6% reported by the same study for the general population of adult men.

The fertility reduction after orchiopexy for bilateral cryptorchidism is more marked, about 38%, or 6 times that of the general population. The basis for the universal recommendation for early surgery is research showing degeneration of spermatogenic tissue and reduced spermatogonia counts after the second year of life in undescended testes. The degree to which this is prevented or improved by early orchiopexy is still uncertain.

A variant is a less serious but chronic condition called intermittent testicular torsion (ITT), characterized by the symptoms of torsion but followed by eventual spontaneous detortion and resolution of pain. Nausea or vomiting may also occur. Though less pressing, such individuals are at significant risk of complete torsion and possible subsequent orchiectomy and the recommended treatment is elective bilateral orchiopexy. Ninety-seven percent of patients who undergo such surgery experience complete relief from their symptoms.

The Sertoli cell-only syndrome patients normally have normal secondary male features and have normal- or small-sized testes.

Penile agenesis is a birth defect in humans, occurring about once in 5–6 million male births, in which a male child is born without a penis.

A partner condition is testicular or gonadal agenesis. This is when a male child is born without gonads and consequently develops no testes. Penile agenesis occurs often as a consequence of Testicular agenesis, but the reverse is never the case. Most patients in both cases have no known family history and usually have an otherwise normal male anatomy.

Sertoli cell only syndrome is likely multifactorial, and characterized by severely reduced or absent spermatogenesis despite the presence of both Sertoli and Leydig cells. A substantial subset of men with this uncommon syndrome have microdeletions in the Yq11 region of the Y chromosome, an area known as the AZF (azoospermia factor) region. Generally speaking, testosterone and LH levels are normal, but due to lack of inhibin, FSH levels are increased.

The appearance of XX males can fall into one of three categories: 1) males that have normal internal and external genitalia, 2) males with external ambiguities, and 3) males that have both internal and external genital ambiguities (true hermaphrodites). External genital ambiguities can include hypospadias, micropenis, and clitoromegaly. On average, the appearance of XX males differs from that of an XY male in that they are smaller in height and weight. Most XX males have small testes, are sterile, and have an increase in maldescended testicles compared to XY males. Some XX male individuals have decreased amounts of body hair and decreased libido. Individuals with this condition sometimes have feminine characteristics, with varying degrees of gynecomastia but with no intra-abdominal Müllerian tissue. According to research at the University of Oklahoma health science centers, despite XX males exhibiting feminine characteristics, their behaviours are usually representative of masculinity in their culture.

At puberty, most affected individuals require treatment with the male sex hormone testosterone to induce development of male secondary sex characteristics such as facial hair and deepening of the voice (masculinization). Hormone treatment can also help prevent breast enlargement (gynecomastia). Adults with this disorder are usually shorter than average for males and are unable to have children (infertile).

The testicle or testis is the male reproductive gland in all animals, including humans. It is homologous to the female ovary. The functions of the testes are to produce both sperm and androgens, primarily testosterone. Testosterone release is controlled by the anterior pituitary luteinizing hormone; whereas sperm production is controlled both by the anterior pituitary follicle-stimulating hormone and gonadal testosterone.

The key affected features of this condition are described in its name.

Scalp: There are raised nodules over the posterior aspect of the scalp, covered by scarred non-hair bearing skin.

Ears: The shape of the pinnae is abnormal, with the superior edge of the pinna being turned over more than usual. The size of the tragus, antitragus and lobule may be small.

Nipples: The nipples are absent or rudimentary. The breasts may be small or virtually absent.

Other features of the condition include:

Dental abnormalities: missing or widely spaced teeth

Syndactyly: toes or fingers may be partially joined proximally

Renal abnormalities: renal hypoplasia, pyeloureteral duplication

Eye abnormalities: Cataract, coloboma of the iris and asymmetric pupils.

Individuals with 5-ARD are born with male gonads, including testicles and Wolffian structures. They can have normal male external genitalia, ambiguous genitalia, or normal female genitalia, but usually tend towards a female appearance. As a consequence, they are often raised as girls, but usually have a male gender identity.

The development of the genital tubercle tissue (which by week 9 of a fetus' gestation becomes either a clitoris or a penis) tends towards a size qualifying it as an ambiguous macroclitoris/micropenis (large clitoris/small penis), and the urethra may attach to the phallus.

If the condition has not already been diagnosed, it usually becomes apparent at puberty around age twelve with primary amenorrhoea and virilization. This may include descending of the testes, hirsutism (facial/body hair considered normal in males - not to be confused with hypertrichosis), deepening of the voice, and enlargement of the clitoris into what would then be classed as a penis.

In adulthood, individuals do not experience male-pattern baldness. As DHT is a far more potent androgen than testosterone alone, virilization in those lacking DHT may be absent or reduced compared to males with functional 5-AR. It is hypothesized that rising testosterone levels at the start of puberty are able to generate sufficient levels of DHT either by the action of 5α-reductase type I (active in the adult liver, non-genital skin and some brain areas) or through the expression of low levels of 5α-reductase type II in the testes.

5-ARD is associated with an increased risk of cryptorchidism and testicular cancer.

The American Fertility Society (now American Society of Reproductive Medicine) Classification distinguishes:

- Class I: Müllerian agenesis (absent uterus).

- Uterus is not present, vagina only rudimentary or absent. The condition is also called Mayer-Rokitansky-Kuster-Hauser syndrome. The patient with MRKH syndrome will have primary amenorrhea.

- Class II: Unicornuate uterus (a one-sided uterus).

- Only one side of the Müllerian duct forms. The uterus has a typical "banana shape" on imaging systems.

- Class III: Uterus didelphys, also uterus didelphis (double uterus).

- Both Müllerian ducts develop but fail to fuse, thus the patient has a "double uterus". This may be a condition with a double cervix and a vaginal partition (v.i.), or the lower Müllerian system fused into its unpaired condition. See Triplet-birth with Uterus didelphys for a case of a woman having spontaneous birth in both wombs with twins.

- Class IV: Bicornuate uterus (uterus with two horns).

- Only the upper part of that part of the Müllerian system that forms the uterus fails to fuse, thus the caudal part of the uterus is normal, the cranial part is bifurcated. The uterus is "heart-shaped".

- Class V: Septated uterus (uterine septum or partition).

- The two Müllerian ducts have fused, but the partition between them is still present, splitting the system into two parts. With a complete septum the vagina, cervix and the uterus can be partitioned. Usually the septum affects only the cranial part of the uterus. A uterine septum is the most common uterine malformation and a cause for miscarriages. It is diagnosed by medical image techniques, i.e. ultrasound or an MRI. MRI is considered the preferred modality due to its multiplanar capabilities as well as its ability to evaluate the uterine contour, junctional zone, and other pelvic anatomy. A hysterosalpingogram is not considered as useful due to the inability of the technique to evaluate the exterior contour of the uterus and distinguish between a bicornuate and septate uterus.

A uterine septum can be corrected by hysteroscopic surgery.

- Class VI: DES uterus.

- The uterine cavity has a "T-shape" as a result of fetal exposure to diethylstilbestrol.

An additional variation is the arcuate uterus where there is a concave dimple in the uterine fundus within the cavity.

A rudimentary uterus is a uterine remnant not connected to cervix and vagina and may be found on the other side of an unicornuate uterus.

Patients with uterine abnormalities may have associated renal abnormalities including unilateral renal agenesis.

A uterine malformation is a type of female genital malformation resulting from an abnormal development of the Müllerian duct(s) during embryogenesis. Symptoms range from amenorrhea, infertility, recurrent pregnancy loss, and pain, to normal functioning depending on the nature of the defect.

A supplemental system of phenotypic grading that uses seven classes instead of the traditional three was proposed by pediatric endocrinologist Charmian A. Quigley et al. in 1995. The first six grades of the scale, grades 1 through 6, are differentiated by the degree of genital masculinization; grade 1 is indicated when the external genitalia is fully masculinized, grade 6 is indicated when the external genitalia is fully feminized, and grades 2 through 5 quantify four degrees of increasingly feminized genitalia that lie in the interim. Grade 7 is indistinguishable from grade 6 until puberty, and is thereafter differentiated by the presence of secondary terminal hair; grade 6 is indicated when secondary terminal hair is present, whereas grade 7 is indicated when it is absent. The Quigley scale can be used in conjunction with the traditional three classes of AIS to provide additional information regarding the degree of genital masculinization, and is particularly useful when the diagnosis is PAIS.

Partial androgen insensitivity syndrome is diagnosed when the degree of androgen insensitivity in an individual with a 46,XY karyotype is great enough to partially prevent the masculinization of the genitalia, but is not great enough to completely prevent genital masculinization. This includes any phenotype resulting from androgen insensitivity where the genitalia is partially, but not completely masculinized. Genital ambiguities are frequently detected during clinical examination at birth, and consequently, a PAIS diagnosis can be made during infancy as part of a differential diagnostic workup.

Pubertal undervirilization is common, including gynecomastia, decreased secondary terminal hair, and / or a high pitched voice. The phallic structure ranges from a penis with varying degrees of diminished size and hypospadias to a slightly enlarged clitoris. Wolffian structures (the epididymides, vasa deferentia, and seminal vesicles) are typically partially or fully developed. The prostate is typically small or impalpable. Müllerian remnants are rare, but have been reported.

The gonads in individuals with PAIS are testes, regardless of phenotype; during the embryonic stage of development, testes form in an androgen-independent process that occurs due to the influence of the SRY gene on the Y chromosome. Cryptorchidism is common, and carries with it a 50% risk of germ cell malignancy. If the testes are located intrascrotally, there may still be significant risk of germ cell malignancy; studies have not yet been published to assess this risk.

Predominantly male phenotypes vary in the degree of genital undermasculinization to include micropenis, chordee, scrotum, and / or pseudovaginal perineoscrotal hypospadias. Impotence may be fairly common, depending on phenotypic features; in one study of 15 males with PAIS, 80% of those interviewed indicated that they had some degree of impotence. Anejaculation appears to occur somewhat independently of impotence; some men are still able to ejaculate despite impotence, and others without erectile difficulties cannot. Predominantly female phenotypes include a variable degree of labial fusion and clitoromegaly. Ambiguous phenotypic states include a phallic structure that is intermediate between a clitoris and a penis, and a single perineal orifice that connects to both the urethra and the vagina (i.e. urogenital sinus). At birth, it may not be possible to immediately differentiate the external genitalia of individuals with PAIS as being either male or female, although the majority of individuals with PAIS are raised male.

Given the wide diversity of phenotypes associated with PAIS, the diagnosis is often further specified by assessing genital masculinization. Grades 2 through 5 of the Quigley scale quantify four degrees of increasingly feminized genitalia that correspond to PAIS.

Grade 2, the mildest form of PAIS, presents with a predominantly male phenotype that presents with minor signs of undermasculinized genitalia, such as isolated hypospadias, which can be severe. Hypospadias may manifest with a partially formed channel from the urethral opening to the glans. Until recently, it was thought that isolated micropenis was not a manifestation of PAIS. However, in 2010, two cases of PAIS manifesting with isolated micropenis were documented.

Grade 3, the most common phenotypic form of PAIS, features a predominantly male phenotype that is more severely undermasculinized, and typically presents with micropenis and pseudovaginal perineoscrotal hypospadias with scrotum.

Grade 4 presents with a gender ambiguous phenotype, including a phallic structure that is intermediate between a clitoris and a penis. The urethra typically opens into a common channel with the vagina (i.e. urogenital sinus).

Grade 5, the form of PAIS with the greatest degree of androgen insensitivity, presents with a mostly female phenotype, including separate urethral and vaginal orifices, but also shows signs of slight masculinization including mild clitoromegaly and / or partial labial fusion.

Previously, it was erroneously thought that individuals with PAIS were always infertile; at least one case report has been published that describes fertile men that fit the criteria for grade 2 PAIS (micropenis, penile hypospadias, and gynecomastia).