The vaginal wall is composed of three layers: the mucosa, which encompasses the epithelium and submucosal stroma; a muscular layer that is in continuity with the uterus; and the adventitia, a dense connective tissue with nerves, veins, and lymphatic channels.1 The vaginal mucosa consists of a nonkeratinized, stratified, and glycogenated squamous epithelium of variable thickness (Figure 2.1). The number of cell layers in the vaginal mucosa varies in response to hormone levels and are separated into deep, intermediate, and superficial layers. The deep layer of squamous epithelium comprises basal and parabasal cells that are vertically oriented with respect to the basement membrane and are responsible for regeneration of the mucosa.1 The intermediate and superficial layers of the mucosa vary in thickness, averaging 10 rows each.1 Intercellular bridges can be found in the intermediate layers of the mucosa, and the cells have basophilic cytoplasm with round or oval nuclei. The superficial rows of cells are polygonal with acidophilic cytoplasm and small, centrally placed nuclei. Underlying the surface epithelium is a submucosal connective tissue with elastic fibers, blood vessels, lymphatics, and rare, stellate stromal cells.

During reproductive years, and especially during ovulation when levels of circulating estrogen are high, the mucosal wall proliferates and matures creating a relatively thick intermediate and superficial layer. In contrast, during menopause when levels of circulating estrogen are low, the mucosa is thin and atrophic.

The upper one-third of the vagina develops from Müllerian origin (paramesonephric ducts) and the lower two-thirds develops from the urogenital sinus. Given the commonality of embryologic development, there is significant overlap among cervical, vulvar, and vaginal pathologies.


The vaginal flora is a diverse microbiome that fluctuates in response to hormonal, chemical, and physical changes throughout a woman’s lifetime. Indolent changes in the vaginal microenvironment occur during menarche, pregnancy, and menopause, sometimes noted by changes in the consistency, color, odor, and extent of vaginal discharge.2 Lactobacillus spp. are part of the normal flora and the most common bacterium isolated from the vagina.2 Bacterial, fungal, and viral infections may exhibit overlapping symptoms encompassed under the umbrella clinical term “vaginitis.” See Chapter 1, for further discussion on infectious dermatoses.

Candida is one of the most common vaginal infections, and the risk of infection is increased by the use of antibiotics, oral or vaginal contraceptives, cancer, and pregnancy.3,4 Patients present with thick, white discharge, pruritus, and erythematous mucosa. Most cases result from infection with Candida albicans, but Candida glabrata may be associated with a vaginitis that is refractory to treatment.5,6 If a vaginal biopsy exhibits neutrophils in the mucosal epithelium with a dense submucosal lymphocytic infiltrate, an infectious process should be suspected. The pseudohyphae that are characteristic of Candida may be identified on a hematoxylin and eosin (H&E)-stained slide, or a fungal stain may assist with identification.


Vaginal cysts are most commonly identified in reproductive-age and postmenopausal women, either incidentally or as a symptomatic mass.7 Cysts may arise from a congenital anomaly in embryologic remnants or are acquired following trauma, persistent inflammation, ectopic endometriotic implants, or at the site of a prior episiotomy.8 Vaginal cysts generally follow an indolent or benign course, but rare reports of malignancy arising in the cystic epithelium have been reported.9,10 See Figure 2.2 for the anatomic locations of vaginal cysts and Table 2.1 for additional details on vaginal cysts.


Müllerian cysts are the most commonly reported vaginal cysts and originate from paramesonephric (Müllerian) remnants. Although they may occur in the lower vagina, the anterolateral walls of the upper vagina are the most frequent location. Müllerian cysts can present over a wide age range (20-66 years) with mild pain, dysuria, discharge, or a palpable mass.12,13,14

Dyspareunia is a rare presenting symptom and may be associated with an abscessed Müllerian cyst.15 The cysts range from 1.4 to 7.0 cm and are lined by bland mucinous, endocervical, tubal, or endometrioid-type epithelium. The overwhelming majority have a benign prognosis; however, there is one report of an adenocarcinoma arising from a Müllerian cyst.9


In contrast to Müllerian cysts, Gartner cysts arise from mesonephric (Wolffian) remnants in the lateral walls of the vagina and typically occur in younger reproductive-age women (23-28 years).7,13 Gartner cysts are generally small (mean, less than 2.0 cm). The cystic epithelium is bland, low columnar to cuboidal, without mucin, and the cytoplasm is eosinophilic or vacuolated.16 Malignant transformation is exceptionally rare, with a single report of clear cell adenocarcinoma arising from a Gartner cyst.10


The Bartholin glands are mucin-secreting glands located posterior to the introitus, bilaterally at the 4:00 and 8:00 positions (see Figure 2.2).17 If the ducts become obstructed, an infection or abscess may occur, leading to enlargement of the gland, cyst development (Figures 2.3A and 2.4A), and pain. Smaller cysts usually heal without treatment, but large cysts may require incision and drainage with subsequent antibiotic treatment. The cyst lining may consist of squamous, transitional, ciliated, or mucinous epithelium (Figures 2.3B-C and 2.4B-C).
While rare, primary Bartholin gland adenocarcinoma can occur and is generally diagnosed in women over 40 years of age. Therefore, in this patient population, the cyst tissue should undergo careful macro- and microscopic review to rule out malignancy. The most frequent histologic subtypes include squamous cell carcinoma, adenocarcinoma, and adenoid cystic carcinoma (Figure 2.5A and B).18,19,20,21,22,23 The proposed criteria for a tumor arising in Bartholin glands include (1) the tumor should demonstrate areas of transition between the tumor cells and the normal gland, (2) the tumor should involve an area of the Bartholin gland, and (3) there should not be any evidence of another primary tumor.19 Refer to Table 2.1 and Chapter 1 for more details on Bartholin glands and associated pathologies.


The Skene glands originate from the urogenital sinus and are embryologically homologous to the male prostate. They are symmetrically located on either side of the distal urethra and function in mucoid secretion to provide lubrication. A Skene duct or Skene gland cyst arises from dilatation of the paraurethral duct or gland, respectively. Cyst development is rare and more commonly found in adults (33-75 years).7,12 Gonorrhea is the most common cause of skenitis and can lead to duct obstruction with cyst formation, urinary obstruction, and pain.24 Rarely, Skene cysts can arise in female neonates as a congenital anomaly.25 The cysts are unilocular and round (Figure 2.6), and the lining is composed of transitional, columnar (Figure 2.7), or squamous epithelium (Figure 2.8).7,12,26 If symptomatic, a large cyst may require surgical intervention.


A squamous inclusion cyst/epithelial inclusion cyst (EIC) is a benign acquired vaginal cyst and may present anywhere in the vagina, most commonly at the site of a prior injury or trauma. One-third of all EICs form at the site of prior obstetric trauma or episiotomy.8
The overlying mucosa invaginates during the healing process and creates a cyst-like cavity filled with keratin debris and is lined by stratified squamous epithelium (Figures 2.9 and 2.10) and metaplasic changes may be seen (Figures 2.11 and 2.12). An EIC is generally small (mean, 1.6 cm) but may cause a mass effect resulting in urinary obstruction or stress incontinence and pain.12 If symptomatic or enlarging, squamous inclusion cysts can be locally excised.8



Tubulosquamous polyps are benign vaginal lesions that develop in both peri- and postmenopausal women (age range, 39-78 years).27 These polyps are believed to originate from ectopic Skene glands. In premenopausal women, the polyp generally arises in the lower vagina and is histologically characterized by mucin-filled cystic spaces lined by squamous epithelium with metaplastic changes. In contrast, tubulosquamous polyps in
postmenopausal women tend to develop in the upper vagina, are polypoid, and contain solid nests of metaplastic squamous epithelium with microcysts.28,29,30 The presence of sebaceous glands within the lesion has also been described.31 Tubulosquamous polyps are rare, and if suspected, immunohistochemical expression of CK7, prostate specific antigen, and/or NKX3.1 supports the diagnosis.27,29,30


In contrast to tubulosquamous polyps, fibroepithelial polyps (FEPs) should appear histologically similar to the adjacent normal vaginal mucosa, albeit polypoid.32,33 The majority of polyps are incidentally discovered in women over a wide age range, and a small subset are symptomatic.34 Some cases are associated with endogenous or exogenous hormone exposure; about 25% of women are pregnant at the time of diagnosis and 10% of women have received some form of exogenous hormonal therapy. FEPs are also discussed in association with genital stromal tumors (see Chapter 1).

Most FEPs are soft to rubbery solitary lesions less than 5 cm but may grow as large as 19 cm.35 During pregnancy, multiple polyps may occur. Often hyperplastic, the overlying squamous epithelium displays normal maturation and surrounds a central fibrovascular core with small stromal blood vessels. The lesion extends to the epithelial-stromal interface and lacks a grenz zone. The multinucleate or stellate stromal cells that are typically
identified in the normal subepithelial connective tissue of the vagina comprise the central core of these polyps and occur in variable quantities to impart a hyper- or hypocellular stroma. The stromal cells give rise to this entity as a result of hormonal influence and will express immunohistochemical markers for desmin, estrogen receptor (ER), and progesterone receptor (PR).34,36 Rarely, FEPs may focally express myogenin.37 Local excision is generally curative. The FEPs that occur during pregnancy will generally regress in the postpartum period or are treated with local excision, if needed.34


Cellular pseudosarcomatous fibroepithelial polyps are variants of benign fibroepithelial polyps with histologic features that may raise concern for a sarcomatous neoplasm. Nucci et al reported a series of pseudosarcomatous FEPs in reproductive-age women, often identified during pregnancy.33,38,39,40,41 It should be noted that the WHO Classification of Tumors, 5th ed. Female Genital Tumors does not recommend the term cellular pseudosarcomatous fibroepithelial polyp and considers this variant as part of the FEP spectrum of disease.41,42 However, the level of cytologic atypia typically observed in these polyps presents a diagnostic pitfall and therefore, will be discussed here.

Cellular pseudosarcomatous FEPs exhibit a hypercellular stroma that merges imperceptibly with the epithelial-stromal interface (a Grenz zone is absent) (Figure 2.13). The background stroma demonstrates a variable amount of collagen (Figure 2.14) and the vessels are generally indistinct; however, thick-walled vessels may be present.

Many cases have multinucleated giant cells and bizarre, pleomorphic, atypical stellate stromal cells, which can help support the diagnosis (Figure 2.15). An increase in mitotic activity is not unusual, often in excess of 10 mitotic figures (MFs) per 10 high-power fields (HPFs), and atypical mitotic figures may be present.38,39,43 The extent of cytologic atypia may be worse and the mitotic activity increased in pregnant patients, suggesting a hormonal influence.38,39 Other occasional findings include an inflammatory infiltrate and/or necrosis.

Although usually a H&E diagnosis, if immunohistochemical studies are performed, the stromal cells are often strongly positive for desmin and do not express cytokeratin or S100.37,38,44 In rare cases, local recurrence may occur following local excision.38 Distant metastatic disease and local tissue destruction have not been reported in cellular pseudosarcomatous FEP.



Condyloma Acuminatum

Condyloma acuminata are human papillomavirus (HPV)-related squamoproliferative lesions, and the majority of condyloma harbor low-risk HPV genotypes 6 and 11.45,46 Although the lesions are more commonly found on the vaginal mucosa of young, reproductive-age women, they may occur in women of any age group. As with all viral-related infections of the lower female genital tract, an increase in the number of sexual partners can increase the likelihood of acquiring HPV and developing vaginal condyloma. Clinically, patients may experience mild discomfort, but generally condyloma are asymptomatic and the polypoid, verrucous, or cauliflower-like protrusions are incidentally found during pelvic examinations.

Histologically, condyloma have papillary stalks emanating from a centralized fibrovascular core and surface keratosis. Small vessels with surrounding scanty stroma push upward through the epithelium and produce surface elevations resulting in undulations or “spikes” (Figure 2.16A). The cytologic characteristics of condyloma are akin to low-grade squamous intraepithelial lesions (LSILs) with koilocytotic atypia (Figure 2.16B).46 The diagnosis of
condyloma based on morphology alone can be challenging. A history of HPV infection or prior cervical dysplasia and high clinical suspicion may be helpful for favoring condyloma (see Pearls & Pitfalls). Additional details for approaching diagnostically challenging squamoproliferative lesions of the anogenital tract are further discussed in the vulvar chapter (see Benign squamous lesions of the vulva).

Condyloma acuminatum have potential for local recurrence after surgical excision. Occasionally, immunosuppressed populations coinfected with high-risk HPV genotypes can lead to carcinogenesis in an otherwise low-grade condyloma.47

Squamous Intraepithelial Lesions

Vaginal intraepithelial neoplasia (VaIN) is a HPV-driven lesion with HPV 16 as the most commonly identified genotype in both the precursor high-grade squamous intraepithelial lesions (VaIN 2-3) and associated HPV-related cancers of the vagina.48,49 The guidelines for diagnosing HPV-related low- and high-grade squamous intraepithelial lesions (VaIN 1 and VaIN 2-3, respectively) of the vagina are similar to the diagnostic algorithms used for cervical and vulvar squamous intraepithelial lesions (SILs) and follow the Lower Anogenital Squamous Terminology Standardization (LAST) criteria.50 Studies have shown that women with a history of HPV-related cervical SILs have an increased risk of vaginal SILs, including the development of high-grade lesions (VaIN 2 and 3) and vaginal cancers.48,51 Tobacco use, number of sexual partners (risk is directly proportional),
and age are also risk factors for developing VaIN, with the majority of VaIN 2-3 cases diagnosed in women over the age of 50 years.52 Clinically, it can be challenging to distinguish between low- and high-grade lesions on colposcopic examination, and therefore, biopsies of lesions are obtained for histologic examination to differentiate between VaIN 1 and VaIN 2-3.48,51

The histomorphology of a low-grade squamous intraepithelial lesion (VaIN 1) is similar to that of other female lower anogenital tract low-grade squamous intraepithelial lesions (LSIL/CIN1). Both LSIL/CIN1 and VaIN 1 are characterized by mild squamous epithelial changes associated with the viral cytopathic effects of HPV. Diagnostic features include enlarged, hyperchromatic, wrinkled nuclei surrounded by perinuclear halos (koilocytes) that may be present throughout the full thickness of the mucosa. Binucleation is a common finding but not specific to LSIL and can occasionally be associated with reactive/reparative changes. Proliferation of the basal/parabasal layer and mitotic figures are restricted to the lower one-third of the mucosa.

Conversely, a vaginal high-grade squamous intraepithelial lesion (VaIN 2-3) exhibits moderate to severe cytologic atypia extending into the upper two-thirds (VaIN 2) and entire full thickness (VaIN 3) of the vaginal mucosa. The nuclei are immature and hyperchromatic with an increased nuclear to cytoplasmic ratio (Figure 2.17 and 2.18). Mitotic activity is increased throughout the mucosa, and atypical mitotic figures may be identified. Treatment for VaIN includes topical therapy (imiquimod, 5-fluorouracil), ablation, or surgical excision, but local recurrence and progression to invasive cancer are not infrequent.53,54

Squamous Cell Carcinoma

Primary vaginal carcinomas are rare, with the majority of cases diagnosed in women over the age of 50 years.55,56 The most common primary vaginal cancer is invasive squamous cell carcinoma and nearly two-thirds of cases are associated with HPV infection (primarily HPV 16).55 Most vaginal cancers are metastatic in origin; therefore, in order to diagnose a primary vaginal cancer the woman should not carry a diagnosis of cervical or vulvar cancer in the preceding 5 years.57 Vaginal bleeding is the most frequent presenting symptom, and the majority of cases originate in the upper third or proximal aspect of the vagina, rendering it difficult to visualize lesions and estimate accurate size or extent of disease on clinical examination.56,58 Squamous cell carcinoma may present as an ulceration with a papillary or warty lesion, or as a firm mass. Invasive squamous cell carcinoma (usual type) is the most common histologic diagnosis58 (Figures 2.19, 2.20 and 2.21), with less common variants including verrucous, basaloid, papillary, and warty.28 (Squamous cell carcinoma is described in more detail in Chapters 1 and 3) When invasion is suspected, but cannot be definitively determined on a superficial biopsy, a note to the clinician may be appropriate: