Symptoms and signs in the newborn can be sepsis, abdominal mass, and respiratory distress. Other abdominopelvic or perineal congenital anomalies frequently prompt radiographic evaluation in the newborn, resulting in a diagnosis of coincident vaginal atresia. Symptoms for vaginal atresia include cyclical abdominal pain, the inability to start having menstrual cycles, a small pouch or dimple where a vaginal opening should be, and pelvic mass when the upper vagina becomes filled with menstrual blood. Signs and symptoms of vaginal atresia or vaginal agenesis can often go unnoticed in females until they reach the age of menstruation. Women may also experience some form of abdominal pain or cramping.

Vaginal atresia can sometimes be diagnosed by physical examination soon after birth. A child with vaginal atresia often has other congenital abnormalities and other tests such as x-ray and tests to evaluate the kidney are done. Findings in adolescents may include abdominal pain, difficulty voiding, and backache, but most present with amenorrhea. Difficulties with sexual intercourse can suggest atresia. In the event that the condition is not caught shortly after birth, vaginal atresia becomes more evident when no menstrual cycle is occurs. If vaginal atresia is suspected by the doctor, a blood test may also be request for any of the previously mentioned syndromes, a magnetic resonance imaging (MRI) test, or an ultrasound. A regular evaluation of children born with an imperforate anus or anorectal malformation should be paired with the assessment of the results from these tests.

The absence of a vagina is a result of vaginal agenesis. Diagnostically, it may look similar to a vaginal obstruction such as can be caused by an imperforate hymen or, less commonly, a transverse vaginal septum.

It is frequently associated with Mayer-Rokitansky-Küstner-Hauser (MRKH) syndrome, in which the most common result is an absent uterus in conjunction with a deformed or missing vagina, despite the presence of normal ovaries and normal external genitalia. It is also associated with cervical agenesis, in which the uterus is present but the uterine cervix is absent.

The situation is most urgent where there is a menstruating uterus with an obstructed uterovaginal outflow, leading to hematometra. In this case prompt medical action is required.

Vaginal hypoplasia can vary in severity from being smaller than normal to being completely absent.

Patients with cervical agenesis typically present in early adolescence, around the time of menarche, with amenorrhea and cyclic pelvic pain caused by the obstruction of menstrual flow from the uterus.

Cervical agenesis is a congenital disorder of the female genital system that manifests itself in the absence of a cervix, the connecting structure between the uterus and vagina. Milder forms of the condition, in which the cervix is present but deformed and nonfunctional, are known as cervical atresia or cervical dysgenesis.

Affected newborns may present with acute urinary retention. In adolescent females, the most common symptoms of an imperforate hymen are cyclic pelvic pain and amenorrhea; other symptoms associated with hematocolpos include urinary retention, constipation, back pain, nausea, and diarrhea.

A transverse septum can form during embryogenesis when the Müllerian ducts fuse improperly to the urogenital sinus. A complete transverse septum will block menstrual flow and is a cause of primary amenorrhea. The accumulation of menstrual debris behind the septum is termed cryptomenorrhea. Some transverse septa are incomplete and may lead to dyspareunia or obstruction in labour. A surgical incision will relieve the situation.

A longitudinal vaginal septum develops during embryogenesis when there is an incomplete fusion of the lower parts of the two Müllerian ducts. As a result, there is a "double vagina". There may be associated duplications of the more cranial parts of the Müllerian derivatives, a double cervix, and either a uterine septum or uterus didelphys (double uterus).

The person with a longitudinal vaginal septum may be asymptomatic and not aware of the condition. If dyspareunia is a problem a simple resection of the septum could be performed.

An imperforate hymen is a congenital disorder where a hymen without an opening completely obstructs the vagina. It is caused by a failure of the hymen to perforate during fetal development. It is most often diagnosed in adolescent girls when menstrual blood accumulates in the vagina and sometimes also in the uterus. It is treated by surgical incision of the hymen.

The symptoms of a cystocele may include:

- a vaginal bulge

- the feeling that something is falling out of the vagina

- the sensation of pelvic heaviness or fullness

- difficulty starting a urine stream

- a feeling of incomplete urination

- frequent or urgent urination

- fecal incontinence

- frequent urinary tract infections

A bladder that has dropped from its normal position and into the vagina can cause some forms of incontinence and incomplete emptying of the bladder.

Hematometra typically presents as cyclic, cramping pain in the midline of the pelvis or lower abdomen. Patients may also report urinary frequency and urinary retention. Premenopausal women with hematometra often experience abnormal vaginal bleeding, including dysmenorrhea (pain during menstruation) or amenorrhea (lack of menstruation), while postmenopausal women are more likely to be asymptomatic. Due to the accumulation of blood in the uterus, patients may develop low blood pressure or a vasovagal response. When palpated, the uterus will typically feel firm and enlarged.

Vesicovaginal fistula, or VVF, is an abnormal fistulous tract extending between the bladder (or vesico) and the vagina that allows the continuous involuntary discharge of urine into the vaginal vault.

In addition to the medical sequela from these fistulas, they often have a profound effect on the patient's emotional well-being.

Hydrocolpos is the distension of the vagina caused by accumulation of fluid due to congenital vaginal obstruction. The obstruction is often caused by an imperforate hymen or less commonly a transverse vaginal septum. The fluid consists of cervical and endometrial mucus or in rare instances urine accumulated through a vesicovaginal fistula proximal to the obstruction. In some cases it is associated with Bardet-Biedl Syndrome. If it occurs in prepubertal girls, it may show up as abdominal swelling. It may be detected by using ultrasound. It may also present at birth as a distended lower abdomen and vagina. It also associated with vaginal atresia.

Complications may include urinary retention, recurring urinary tract infections and incontinence. The anterior vaginal wall may actually protrude though the vaginal introitus (opening). This can interfere with sexual activity. Recurrent urinary tract infections are common for those who have urinary retention. In addition, though cystocele can be treated, some treatments may not alleviate troubling symptoms, and further treatment may need to be performed. Cystocele may effect the quality of life. Women who have cystocele tend to avoid leaving their home and social situations. The resulting incontinence puts women at risk of being placed in a nursing home or long term care facility.

Mild cases may simply produce a sense of pressure or protrusion within the vagina, and the occasional feeling that the rectum has not been completely emptied after a bowel movement. Moderate cases may involve difficulty passing stool (because the attempt to evacuate pushes the stool into the rectocele instead of out through the anus), discomfort or pain during evacuation or intercourse, constipation, and a general sensation that something is "falling down" or "falling out" within the pelvis. Severe cases may cause vaginal bleeding, intermittent fecal incontinence, or even the prolapse of the bulge through the mouth of the vagina, or rectal prolapse through the anus. Digital evacuation, or, manual pushing, on the posterior wall of the vagina helps to aid in bowel movement in a majority of cases of rectocele. Rectocele can be a cause of symptoms of obstructed defecation.

Vesicovaginal fistula (VVF) is a subtype of female urogenital fistula (UGF).

A rectocele ( ) or posterior vaginal wall prolapse results when the rectum herniates into or forms a bulge in the vagina. Two common causes of this defect is: childbirth, and hysterectomy. Rectocele also tends occur with other forms of pelvic organ prolapse such as enterocele, sigmoidocele and cystocele.

Although the term applies most often to this condition in females, males can also develop. Rectoceles in men are uncommon, and associated with prostatectomy.

Vaginal hypoplasia is the underdevelopment or incomplete development of the vagina. Vaginal hypoplasia can vary in severity from being smaller than normal to being completely absent. The absence of a vagina is a result of vaginal agenesis. Diagnostically, it may look similar to a vaginal obstruction. It is frequently associated with Mayer-Rokitansky-Küstner-Hauser (MRKH) syndrome, in which the most common result is an absent uterus in conjunction with a deformed or missing vagina, despite the presence of normal ovaries and normal external genitalia. It is also associated with cervical agenesis, in which the uterus is present but the uterine cervix is absent.

Hematometra or hemometra is a medical condition involving collection or retention of blood in the uterus. It is most commonly caused by an imperforate hymen or a transverse vaginal septum.

Individuals with complete androgen insensitivity syndrome (grades 6 and 7 on the Quigley scale) are born phenotypically female, without any signs of genital masculinization, despite having a 46,XY karyotype. Symptoms of CAIS do not appear until puberty, which may be slightly delayed, but is otherwise normal except for absent menses and diminished or absent secondary terminal hair. Axillary hair (i.e. armpit hair) fails to develop in one third of all cases. External genitalia is normal, although the labia and clitoris are sometimes underdeveloped. The vaginal depth varies widely, but is typically shorter than unaffected women; one study of eight women with CAIS measured the average vaginal depth to be 5.9 cm (vs. 11.1 ± 1.0 cm for unaffected women ). In some extreme cases, the vagina has been reported to be aplastic (resembling a "dimple"), though the exact incidence of this is unknown.

The gonads in these women are not ovaries, but instead, are testes; 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. They may be located intra-abdominally, at the internal inguinal ring, or may herniate into the labia majora, often leading to the discovery of the condition. Testes in affected women have been found to be atrophic upon gonadectomy. Testosterone produced by the testes cannot be directly used due to the mutant androgen receptor that characterizes CAIS; instead, it is aromatized into estrogen, which effectively feminizes the body and accounts for the normal female phenotype observed in CAIS.

Immature sperm cells in the testes do not mature past an early stage, as sensitivity to androgens is required in order for spermatogenesis to complete. Germ cell malignancy risk, once thought to be relatively high, is now thought to be approximately 2%. Wolffian structures (the epididymides, vasa deferentia, and seminal vesicles) are typically absent, but will develop at least partially in approximately 30% of cases, depending on which mutation is causing the CAIS. The prostate, like the external male genitalia, cannot masculinize in the absence of androgen receptor function, and thus remains in the female form.

The Müllerian system (the fallopian tubes, uterus, and upper portion of the vagina) typically regresses due to the presence of anti-Müllerian hormone originating from the Sertoli cells of the testes. These women are thus born without fallopian tubes, a cervix, or a uterus, and the vagina ends "blindly" in a pouch. Müllerian regression does not fully complete in approximately one third of all cases, resulting in Müllerian "remnants". Although rare, a few cases of women with CAIS and fully developed Müllerian structures have been reported. In one exceptional case, a 22-year-old with CAIS was found to have a normal cervix, uterus, and fallopian tubes. In an unrelated case, a fully developed uterus was found in a 22-year-old adult with CAIS.

Other subtle differences that have been reported include slightly longer limbs and larger hands and feet due to a proportionally greater stature than unaffected women, larger teeth, minimal or no acne, well developed breasts, and a greater incidence of meibomian gland dysfunction (i.e. dry eye syndromes and light sensitivity).

A vaginal obstruction is often caused by an imperforate hymen or, less commonly, a transverse vaginal septum. A sign of vaginal obstruction is hydrocolpos, that is, accumulation of watery fluid within the vagina. It may extend to become "hydrometrocolpos", that is, accumulation of watery fluid within the vagina as well as within the uterus.

All forms of androgen insensitivity, including CAIS, are associated with infertility, though exceptions have been reported for both the mild and partial forms.

CAIS is associated with a decreased bone mineral density. Some have hypothesized that the decreased bone mineral density observed in women with CAIS is related to the timing of gonadectomy and inadequate estrogen supplementation. However, recent studies show that bone mineral density is similar whether gonadectomy occurs before or after puberty, and is decreased despite estrogen supplementation, leading some to hypothesize that the deficiency is directly attributable to the role of androgens in bone mineralization.

CAIS is also associated with an increased risk for gonadal tumors (e.g. germ cell malignancy) in adulthood if gonadectomy is not performed. The risk of malignant germ cell tumors in women with CAIS increases with age and has been estimated to be 3.6% at 25 years and 33% at 50 years. The incidence of gonadal tumors in childhood is thought to be relatively low; a recent review of the medical literature found that only three cases of malignant germ cell tumors in prepubescent girls have been reported in association with CAIS in the last 100 years. Some have estimated the incidence of germ cell malignancy to be as low as 0.8% before puberty.

Vaginal hypoplasia, a relatively frequent finding in CAIS and some forms of PAIS, is associated with sexual difficulties including vaginal penetration difficulties and dyspareunia.

At least one study indicates that individuals with an intersex condition may be more prone to psychological difficulties, due at least in part to parental attitudes and behaviors, and concludes that preventative long-term psychological counseling for parents as well as for affected individuals should be initiated at the time of diagnosis.

Lifespan is not thought to be affected by AIS.

There are several forms of imperforate anus and anorectal malformations. The new classification is in relation of the type of associated fistula.

The classical Wingspread classification was in low and high anomalies:

- A low lesion, in which the colon remains close to the skin. In this case, there may be a stenosis (narrowing) of the anus, or the anus may be missing altogether, with the rectum ending in a blind pouch.

- A high lesion, in which the colon is higher up in the pelvis and there is a fistula connecting the rectum and the bladder, urethra or the vagina.

- A persistent cloaca (from the term cloaca, an analogous orifice in reptiles and amphibians), in which the rectum, vagina and urinary tract are joined into a single channel.

Imperforate anus is usually present along with other birth defects—spinal problems, heart problems, tracheoesophageal fistula, esophageal atresia, renal anomalies, and limb anomalies are among the possibilities.

Vaginal flatulence is an emission or expulsion of air from the vagina. It may occur during or after sexual intercourse or during other sexual acts, stretching or exercise. The sound is somewhat comparable to flatulence from the anus but does not involve waste gases and thus often does not have a specific odor associated. Slang terms for vaginal flatulence include vart, queef, and fanny fart (mostly British).