Vaginal agenesis may be isolated, or may be part of the Mayer–Rokitansky–Küster–Hauser syndrome in association with uterine agenesis.

Failure of fusion of the two Müllerian ducts leads to vaginal duplication, which may occur in isolation, or with duplication of the uterus as well.

If fusion occurs, but the septum is not resorbed, longitudinal vaginal septum is present.

Transverse vaginal septum occurs due to failure of resorption of the Müllerian septum at the interface of the urogenital sinus and fused Müllerian ducts [1]. A specimen from an excision of a transverse vaginal septum may show squamous epithelium on the more caudal aspect and columnar epithelium on the more rostral.

Imperforate hymen may present in childhood as mucocolpos, or not show up until menarche as hematocolpos. Hymenal tissue is lined by nonkeratinizing squamous epithelium.

During embryogenesis, the urogenital sinus meets up with the fused Müllerian ducts. At birth, the lower genital tract is lined by squamous epithelium extending up the vagina to the squamo-columnar junction of the cervix. While it had been believed that this was urogenital squamous epithelium replacing any glandular epithelium that had been present in the upper vagina, more recently, some investigators have put forth that the upper vaginal squamous epithelium is derived from Müllerian epithelium [3]. Either spontaneously, or due to an exogenous interference with embryogenesis such as diethylstilbestrol (DES) exposure, remnants of glands may remain in the vaginal submucosa (adenosis), and over time, are replaced by metaplastic squamous epithelium (Fig. 4.1).

Müllerian cysts may arise from foci of adenosis. They are the most common vaginal cysts and may be symptomatic owing to their larger size, with symptoms including sensation of mass, pain, dyspareunia, discharge, and urinary symptoms [4]. They can occur anywhere in the vagina. Lining is variable, typical of the multipotential Müllerian epithelium, and hence mucinous, tubal, endometrioid or squamous epithelium may be seen (Fig. 4.2a).

The mesonephric ducts regress during embryogenesis of a female. Remnants can form cysts. These cysts are generally located along the lateral vagina, in the location of the mesonephric ducts. They tend to be smaller and less symptomatic than Müllerian cysts [4]. They are lined by a cuboidal non-mucinous epithelium and may contain eosinophilic secretions (Fig. 4.2b).

Mucinous cysts are often located in the vestibule. They may be either congenital or acquired and are thought to arise from minor vestibular glands (Fig. 4.2c).

Squamous inclusion cysts are usually localized to prior surgery such as episiotomy, but can occur in any vaginal location. Histologically, they are lined by squamous epithelium, and the cheesy contents are histologically seen to be keratinaceous debris (Fig. 4.2d).

Endometriosis may be cystic or solid and tends to occur in sites of prior surgery such as episiotomy, or trauma, lending credence to the implantation theory. Symptoms may be cyclic. Histologically, endometrial glandular epithelium and stroma must be present to confirm the diagnosis for the pathologist (Fig. 4.3).

This is a rare self-limiting condition where multiple vaginal blebs are formed. Symptoms may include pressure, with relief if the blebs rupture during intercourse or examination [4]. The condition is thought to be related to trichomonas or bacterial vaginosis [5]. The lesions are rarely biopsied, but consistent of empty gas-filled subepithelial spaces [6].