Vaginal atresia is a congenital defect resulting in uterovaginal outflow tract obstruction. It occurs when the caudal portion of the vagina, contributed by the urogenital sinus, fails to form. This caudal portion of the vagina is replaced with fibrous tissue. Vagina atresia and agenesis are congenital anomalies of the female genitourinary tract and may occur as an isolated developmental defect (extremely rare) or as part of a complex of anomalies (more common). Examples of some of these associations are as follows:
In 1998, the American Society for Reproductive Medicine classified the uterine anatomic types as müllerian anomalies or vaginal anomalies. According to this classification system, vaginal atresia is an anomaly classified as type I, which refers to agenesis and hypoplasia of the uterus.  As a consequence, vaginal atresia is occasionally termed müllerian agenesis.
The most common clinical presentation of type I müllerian anomalies is vaginal or müllerian agenesis, which occurs in conjunction with an absent uterus (ie, MRKH syndrome). Renal anomalies, which may include unilateral agenesis of the kidney, ectopic kidneys, horseshoe kidney, and crossed-fused ectopia, occur in 30% of patients with MRKH syndrome. Associated skeletal anomalies may include anomalies found in Klippel-Feil syndrome (ie, aberrations of cervicothoracic somite development), which manifest as fused vertebrae or other variants. Anomalies of the ribs and limbs are also encountered.
Variants of vaginal atresia, formerly called partial vaginal agenesis, are more correctly classified as variants of a transverse vaginal septum. These variants and other developmental variants, such as obstructed duplications of the uterovaginal tract, occur on the basis of other pathophysiologic events and should be treated as separate entities.
Each examination of a newborn should include an inspection of the genitalia, as absence of the vagina or atresia could be detected during this simple evaluation. Delayed detection is common and can result in major risk to the female patient because of associated urinary tract anomalies. Early detection is possible if healthcare providers include a genital examination as part of their well-child examination.
Surgical management of vaginal atresia has been described in the European literature since the turn of the century. In the United States, Baldwin was the first to describe construction of a neovagina using an intestinal graft. As the technique became popular, the potential for clinically significant morbidity and mortality became evident. In 1940, Masson reported two deaths,  which provided the impetus to consider the skin-graft technique McIndoe and Counsellor first reported. 
Vaginal reconstruction techniques may be required in numerous congenital disorders. The choice of operation and outcome critically depend on correct identification of the underlying disorder. Three basic categories of anomalies must be distinguished: vaginal agenesis and its variants, ambiguous genitalia, and imperforate anus and urogenital sinus variants. Optimal medical and surgical management require familiarity with these conditions.
A female infant with a normal perineum has bilateral labial mounds. Readily identifiable discrete structures include clitoral tissue at the most anterior aspect of the introitus, a urethral opening, and a hymenal ring. The anal opening normally is located midway between the posterior confluence of the labia and the tip of the coccyx. Labial fusion may obscure the anatomy of some patients but is not a suggestive finding unless the fusion is posterior and the clitoris is enlarged anteriorly. This configuration suggests congenital adrenal hyperplasia.
The differential diagnosis of ambiguous genitalia and the defects of hindgut development should be considered in the presence of clinically significant anatomic variations. The variant features commonly encountered with ambiguous genitalia include the following:
Rugal folds over the labia
Mass in an apparent labium
Excess clitoral tissue
Features suggestive of anorectal and genitourinary tract malformations include the following:
Urogenital sinus (one common vaginal and urethral opening) with a normal anal opening
Anterior anal opening (imperforate anus with perineal fistula)
Cloacal malformation (a single shared vaginal, urethral, and anal opening)
Normal reproductive organ development in male and female individual requires the timely coordination of the following three discrete but interdependent systems:
Internal ductal system
In the female embryo, the absence of testes and the consequent absence of both androgens and müllerian-inhibiting substance (MIS) allow ongoing development and differentiation of the müllerian duct system with regression of the wolffian ducts. The müllerian duct is identifiable by 6 weeks' gestation in both male and female individuals. This duct elongates and reaches the urogenital sinus by 9 weeks' gestation, thus forming the uterovaginal canal.
The two müllerian ducts proceed caudad to cephalad to the uterine fundus and fuse. Bilateral endodermal invaginations (ie, sinovaginal bulbs) form as the müllerian tubercles regress. Cephalic growth of the sinovaginal bulb is completed at 15-26 weeks' gestation, and fusion of the sinovaginal bulb with the vaginal cord forms the vaginal plate.
Although controversy surrounds the development of a patent genital tract, canalization of the uterovaginal canal is believed to occur from the caudal to the cephalic aspect, with an epithelial lining derived from the urogenital sinus. Vaginal development is completed by 5 months' gestation. Mesenchyme surrounding these structures develops into the musculature of the genital tract. Cephalic remnants of the müllerian duct form the fallopian tubes.
Given this developmental scheme, pathophysiologic events resulting in a septate uterus can be attributed to failure of the septum to regress between the fused müllerian ducts. Arcuate, bicornuate, or didelphic uteri can be attributed to incomplete fusion of the müllerian ducts.
Uterovaginal atresia in patients with MRKH syndrome is best explained by the failure of the caudal development of the müllerian ducts. Failures at the level of the vaginal plate may explain the variants of transverse vaginal septum. Although the vagina is embryologically derived from structures of both the müllerian and urogenital sinuses, how much each anlage contributes to final normal development remains unclear.
The specific molecular mechanisms leading to failure of vaginal development have not been elucidated. Multiple developmental pathways share a critical event that may promote or interfere with normal development. Evidence suggests that these regulating factors may involve paracrine or autocrine signals and alterations in the anlage or matrix of the developing organs.
A pattern of genetic transmission has not been documented and has been refuted by the discordant occurrence of vaginal atresia in three pairs of monozygotic twins. Patients with MRKH syndrome and vaginal atresia are phenotypically and genotypically female with a 46,XX karyotype. However, a familial association suggests autosomal dominant transmission of a mutant gene by male relatives. 
Etiologic factors that Knab implicated in defective organogenesis include the following  :
Inappropriate production of MIS in the female embryonic gonad
Regional absence or deficiency of estrogen receptors in the lower müllerian duct structures
Arrest of müllerian duct development by a teratogenic agent
Mesenchymal inductive defect
Sporadic gene mutation
Vaginal atresia is estimated to occur in 1 in 5000-10,000 live female births. The anomaly is often undetected until adolescence, when primary amenorrhea or abdominal pain due to an obstructed uterovaginal tract prompts a diagnostic evaluation.  Vaginal atresia is reported to be the second most common cause of primary amenorrhea in tertiary care centers. 
Transverse vaginal septum, formerly called partial vaginal agenesis, is relatively uncommon, with a reported incidence of 1 in 70,000 females. 
Variations in patients' anatomic findings and the lack of a standardized surgical technique complicate the outcomes and prognostication. Reconstruction for vaginal atresia is frequently reported with other conditions that result in an abnormal perineum (ie, ambiguous genitalia and various anomalies ranging from urogenital sinus to cloaca). Therefore, accurate comparison of outcomes is difficult.
In addition, gender-identify issues in patients treated for ambiguous genitalia occasionally confound the patient's satisfaction from a cosmetic and functional standpoint. An increasing focus on the functional and psychological aspects of these reconstructive operations may help in identifying patients who are best suited to receive specific surgical techniques. This focus may also help in delineating the timing of interventions.
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