Clinical overview
Cysts of the female genital tract are among the commonest findings in gynaecological practice, ranging from incidental, asymptomatic lesions found on a routine speculum examination or pelvic ultrasound to painful, infected or — rarely — malignant masses. For the registrar, the value of this objective is precisely in learning to read a cyst pathologically: a cyst is not a diagnosis but a morphological category (a fluid-filled, epithelium- or membrane-lined cavity), and the clinical meaning depends entirely on where it sits along the tract, what lines it, what fills it, and what gave rise to it. The same word — "cyst" — covers a benign embryological remnant on the vaginal wall, a tense Bartholin abscess in the vulva, a physiological follicular cyst on the ovary, and a unilocular serous cystadenoma that may harbour borderline change. Understanding the gross and microscopic features lets you separate the trivial from the sinister at the bedside, on the scan, and down the microscope.
This is a "describe the pathological features" objective, so the weight sits in Core knowledge — gross morphology, lining epithelium, contents, and the developmental or acquired mechanism for each lesion, site by site from vulva to ovary. But every cyst still demands a coherent assessment (is it benign or does it need malignancy work-up?) and a management principle. In the South African setting two themes run through the whole topic: the very high background prevalence of HIV, which alters the natural history of infective and HPV-driven lesions and raises the index of suspicion for cervical pathology; and the reality of NHLS histopathology turnaround and access, which shapes how aggressively we biopsy versus observe. We will keep WHO-2020 pathology terminology throughout. This chapter links closely to genital-anatomy, fibroids, adnexal-mass-in-pregnancy, ultrasound-malignancy-signs and the screening pathway in cervical-screening-sa.
Core knowledge
A practical way to organise the pathology is developmental (embryological remnant) versus retention versus inflammatory/infective versus functional (physiological) versus neoplastic, applied at each anatomical site. The defining features are always the same triad: lining epithelium, wall, and contents.
Vulval cysts
Figure D1.1 — Genital-tract cysts by site: vulva (Bartholin, epidermoid, Skene), vagina (Gartner, Müllerian), cervix (Nabothian) and adnexa — location as the first diagnostic clue.
- Bartholin gland cyst. The greater vestibular (Bartholin) glands lie at 4 and 8 o'clock at the posterior introitus; they secrete mucus through a duct opening into the vestibule. Obstruction of the duct produces a retention cyst — a unilocular, tense swelling in the posterior labium majus, lined by transitional/squamous epithelium of the duct (the acinar mucinous epithelium is usually destroyed by pressure atrophy). Contents are sterile mucoid fluid. Secondary infection produces a Bartholin abscess — painful, fluctuant, erythematous, often polymicrobial (anaerobes, coliforms; historically Neisseria gonorrhoeae and Chlamydia trachomatis, so STI co-testing matters in the SA/HIV context). A solid or persistent "Bartholin mass" in a woman over 40 must raise the possibility of Bartholin gland carcinoma and be biopsied, not simply drained.
- Epidermal (epidermoid) inclusion cyst. The commonest vulval cyst overall: a keratin-filled cyst lined by stratified squamous epithelium with a granular layer, often from traumatic implantation of epidermis (e.g. after episiotomy or female genital cutting). Gross: small, firm, yellow-white, cheesy keratin content.
- Cyst of the canal of Nuck (hydrocele of the canal of Nuck). A persistent processus vaginalis (the female homologue of a patent processus) producing a cyst in the inguinal/labial region lined by mesothelium — a peritoneal remnant.
- Mucous (mucinous vestibular) cysts of the vestibule, lined by columnar mucinous epithelium of urogenital sinus origin.
Vaginal cysts
Figure D1.2 — Origin explains location: mesonephric/Wolffian (Gartner), paramesonephric/Müllerian and epithelial-inclusion cysts, and the lining/contents each produces.
- Gartner duct cyst. The classic mesonephric (Wolffian) remnant: arises from the embryonic mesonephric duct running along the anterolateral vaginal wall. Lining is low cuboidal/columnar, non-mucinous, non-ciliated epithelium; contents are thin and watery. Usually small and asymptomatic; large ones may cause dyspareunia or obstruct. Their anterolateral position and non-mucinous lining distinguish them from Müllerian cysts.
- Müllerian (paramesonephric) cyst. Lined by mucinous, ciliated or endocervical-type epithelium, reflecting Müllerian origin; can occur anywhere in the vagina.
- Epidermal inclusion cyst. The commonest acquired vaginal cyst, typically posterior wall, at the site of previous obstetric trauma or surgical repair; squamous-lined, keratin-filled — the same pathology as its vulval counterpart.
- Endometriotic cyst / implant in the vaginal wall (rare) — lined by endometrial glands and stroma with haemosiderin-laden macrophages.
Cervical cysts
- Nabothian cyst. The prototypical retention cyst and an entirely benign, near-ubiquitous finding. During the physiological transformation of the cervix, squamous metaplasia overgrows the openings of endocervical (mucous) glands within the transformation zone; trapped mucus distends the gland into a smooth, dome-shaped, often translucent cyst lined by flattened endocervical mucinous columnar epithelium. They may be single or multiple, range from millimetres to a couple of centimetres, and require no treatment. Their relevance is reassurance and not mistaking them for anything sinister.
- Tunnel clusters and mesonephric remnants/hyperplasia of the deep lateral cervix are benign mimics that occasionally cause diagnostic difficulty on histology.
- It is worth contrasting these benign cervical cysts with HPV-driven squamous pathology — LSIL/HSIL (WHO 2020 terminology, equivalent to CIN 1 / CIN 2–3) — covered in hpv-pathology and cin-pathophysiology: cysts are not premalignant, but cervical sampling/screening still applies to the woman as a whole, especially if HIV-positive.
Uterine (myometrial / endometrial) cysts
True uterine "cysts" are uncommon; the lesions that look cystic are usually cystic degeneration within a leiomyoma (see fibroids) — a fibroid that outgrows its blood supply undergoes hyaline then cystic/myxoid degeneration, producing fluid-filled spaces within an otherwise solid mass. Adenomyotic cysts (cystic adenomyosis) are rare, blood-filled cavities lined by endometrial tissue within the myometrium.
Fallopian tube and paratubal cysts
- Hydatid cyst of Morgagni. A small, pedunculated, thin-walled paramesonephric (Müllerian) remnant hanging near the fimbrial end, lined by ciliated tubal-type epithelium with clear serous fluid — a benign incidental finding at laparoscopy or section.
- Paratubal/paraovarian cysts in the broad ligament are commonly mesonephric or mesothelial in origin.
- Hydrosalpinx is a distended, fluid-filled tube following inflammatory occlusion (e.g. post-PID, post-tubal infection) — gross "retort-shaped" dilatation with a thin, attenuated, flattened epithelial lining and loss of plicae; the SA relevance is the high burden of pelvic infection and HIV-associated genital tract disease.
Ovarian cysts — the core of the topic
Figure D1.3 — Benign or act now? Bartholin cyst vs abscess, the >40-year Bartholin mass that needs biopsy, and simple vs complex ovarian cysts on ultrasound.
These are the cysts of greatest clinical weight, and the registrar must separate functional, benign neoplastic, endometriotic, inflammatory and malignant categories.
Functional (physiological) cysts — not neoplasms:
- Follicular cyst. A Graafian follicle that fails to ovulate and continues to grow; thin-walled, unilocular, filled with clear serous fluid, lined by granulosa cells (inner) and theca interna (outer). Usually <5–6 cm and regress spontaneously over 1–2 cycles.
- Corpus luteum cyst. A corpus luteum that fails to involute or bleeds into its cavity; thicker, often crenated yellow (luteinised) wall, may contain altered blood. Can rupture and bleed, mimicking ectopic pregnancy.
- Theca lutein cysts. Bilateral, multiple, due to markedly elevated β-hCG — classically in complete hydatidiform mole / GTD and multiple pregnancy or ovulation induction. Their association with molar disease links this topic to gtd-pathology and gtd-diagnosis.
- A note on terminology: the polycystic ovary of PMOS (formerly PCOS) does not contain pathological cysts — these are arrested antral follicles, not true cysts, a point clarified in the 2026 consensus rename (see hyperandrogenism).
Benign neoplastic (epithelial and germ-cell) cysts:
- Serous cystadenoma. Typically unilocular, thin-walled, filled with clear straw-coloured serous fluid; lined by a single layer of ciliated, tubal-type columnar epithelium; may show psammoma bodies. Often bilateral.
- Mucinous cystadenoma. Tends to be large, multiloculated, filled with viscous mucin; lined by tall mucin-secreting columnar (endocervical- or intestinal-type) epithelium. Rupture can rarely seed pseudomyxoma peritonei (more often appendiceal in origin).
- Mature cystic teratoma (dermoid cyst). The commonest ovarian neoplasm in young women: a germ-cell tumour containing differentiated ectoderm, mesoderm and endoderm. Gross: a cyst filled with sebum, hair and sometimes teeth/bone, with a Rokitansky protuberance (the solid nodule from which hair/teeth arise). Lined by skin with adnexal structures. Risk of torsion; rare malignant (squamous) transformation in older women.
Endometriotic cyst ("chocolate cyst" / endometrioma). Cyclical bleeding into an endometriotic implant produces a cyst with a thick, fibrotic, often densely adherent wall, filled with altered "chocolate"-coloured old blood; lining shows endometrial glands and stroma with abundant haemosiderin-laden macrophages (which may become attenuated). Associated with endometriosis-associated clear-cell and endometrioid carcinomas in a minority over time.
Malignant / borderline cystic tumours. Cystadenocarcinomas and borderline tumours show complex features that distinguish them from benign cysts: solid components, papillary projections, thick irregular septa (>3 mm), internal vascularity, ascites and bilaterality — the morphological substrate of the ultrasound rules in ultrasound-malignancy-signs. Microscopically, borderline tumours show epithelial stratification and atypia without stromal invasion, while carcinoma shows frank invasion.
Assessment
Pathological description drives the work-up: the question at every site is benign retention/developmental remnant versus a lesion needing exclusion of malignancy.
- History and examination. Site, duration, pain, change with cycle (endometrioma, corpus luteum), post-coital or post-surgical onset (inclusion cyst), and red-flag features (rapid growth, weight loss, abdominal distension, postmenopausal status). Vulval/vaginal cysts are usually a visual/palpable diagnosis; a hard, fixed, ulcerated or bleeding vulval "cyst", or any Bartholin mass over 40, mandates biopsy.
- Imaging. Transvaginal ultrasound is the single most useful tool for adnexal cysts: a thin-walled, anechoic, unilocular cyst with no solid component is reassuringly benign, whereas multilocularity, solid areas, papillary projections, thick septa and vascularity are concerning (the basis of pattern-recognition and risk models). MRI characterises indeterminate masses (fat in a dermoid, the T2 shading of an endometrioma).
- Tumour markers. CA-125 (epithelial), AFP/β-hCG/LDH (germ-cell tumours in young women), and the RMI (Risk of Malignancy Index = ultrasound score × menopausal status × CA-125) to triage. In premenopausal women remember CA-125 is non-specific (raised by endometriosis, PID, fibroids, menstruation).
- SA-specific work-up. With high HIV prevalence, infective and inflammatory pelvic pathology (tubo-ovarian abscess, hydrosalpinx) is commoner and TB of the genital tract must be considered in atypical adnexal masses/ascites. Histopathology is processed through NHLS; turnaround and access influence whether a lesion is observed, sampled in clinic, or taken straight to theatre.
- The natural history matters: most functional ovarian cysts in premenopausal women resolve, so a simple cyst is rescanned (typically at ~6 weeks/next cycle) rather than removed.
Management
Management follows directly from the pathology — observe the benign, drain/treat the infected, and apply oncological pathways to the suspicious.
- Benign developmental/retention cysts (Gartner, Müllerian, nabothian, hydatid of Morgagni): reassure and leave; excise only if symptomatic or diagnostically uncertain.
- Bartholin cyst/abscess: symptomatic cysts and abscesses are managed by marsupialisation or Word catheter insertion (preserving gland function) rather than simple incision (which recurs); send pus for culture/STI testing; biopsy any solid component or any Bartholin mass in a woman over 40 to exclude carcinoma.
- Functional ovarian cysts: expectant management with interval ultrasound; persistent or symptomatic cysts may need laparoscopic cystectomy. Postmenopausal simple cysts that are small are commonly monitored; larger or complex ones are referred.
- Endometrioma: managed within the endometriosis pathway (medical suppression and/or laparoscopic cystectomy, balancing symptom relief against ovarian reserve).
- Suspicious/complex or postmenopausal cysts: refer for gynaecological-oncology MDT assessment; surgery aims at intact removal and proper staging when malignancy is possible. The cysts that turn out to be early-stage epithelial tumours feed into the surgical-staging and adjuvant pathways discussed in endometrial-carcinoma and the broader oncology objectives.
- Where a "cyst" is actually a manifestation of malignancy elsewhere in the tract, definitive care follows the relevant disease-specific protocols — cervical chemoradiation with image-guided brachytherapy and systemic immunotherapy (KEYNOTE-A18/826, dostarlimab/RUBY, pembrolizumab+lenvatinib), and GTN chemotherapy for trophoblastic disease — none of which apply to a simple benign cyst, but all of which are the reason we take "complex" morphology seriously.
Red flags / pitfalls
- Calling every adnexal cyst "functional". A persistent, complex or postmenopausal cyst is a neoplasm until proven otherwise — do not over-reassure.
- Draining a Bartholin "cyst" in an older woman without biopsy — Bartholin gland carcinoma is rare but lethal when missed; any solid component or persistent mass over 40 needs histology.
- Mistaking a corpus luteum cyst rupture for an ectopic (and vice versa) — correlate β-hCG, ultrasound and haemodynamics.
- Theca-lutein cysts without checking β-hCG — bilateral multicystic ovaries with very high β-hCG point to molar/GTD (see gtd-diagnosis); do not operate on the ovaries.
- Treating polycystic ovarian morphology as "cysts" to be removed — they are arrested antral follicles (PMOS/formerly PCOS), an endocrine-metabolic problem, not surgical cysts.
- Forgetting the SA/HIV context — higher rates of tubo-ovarian abscess, hydrosalpinx and genital TB; lower threshold to consider infection and to act on cervical screening abnormalities in HIV-positive women.
- Rupturing a mucinous cystadenoma carelessly — spillage and the (rare) pseudomyxoma association argue for careful, ideally intact, removal.
Evidence anchors
- WHO Classification of Tumours of the Female Genital Tract, 5th edition (2020) — the source of truth for the histological typing and terminology of all genital tract cysts and tumours used throughout this chapter, including the WHO-2020 squamous terminology (LSIL/HSIL, equivalent to CIN 1 / CIN 2–3; HPV-associated vs HPV-independent) referenced where cervical pathology is contrasted with benign nabothian cysts.
- RCOG Green-top Guideline No. 62 — Suspected Ovarian Masses in Premenopausal Women and RCOG Green-top Guideline No. 34 — Ovarian Cysts in Postmenopausal Women — assessment, ultrasound morphology, RMI/CA-125 triage and the observe-versus-refer thresholds applied in the Assessment and Management sections.
- NICE CG122 — Ovarian Cancer: Recognition and Initial Management and NICE NG12 — Suspected Cancer: Recognition and Referral — pathways for escalating a complex or suspicious adnexal cyst to oncology.
- ACOG Practice Bulletin 174 — Evaluation and Management of Adnexal Masses (2016, reaffirmed) — cross-reference for the work-up and characterisation of adnexal cystic masses.
- South African cervical cancer screening — SASOG / BetterGyn Clinical Guideline (2024) with NDoH National Cervical Cancer Screening Policy and the WHO Cervical Cancer Elimination Strategy (90-70-90 by 2030) — relevant for the woman in whom a benign cervical (nabothian) cyst is found, ensuring she is appropriately screened, with HIV-positive women screened at HIV diagnosis and more frequently regardless of age.
- For trophoblastic disease causing theca-lutein cysts, RCOG Green-top Guideline No. 38 — Gestational Trophoblastic Disease anchors the molar/GTN context (see gtd-diagnosis).
Uncertainty flagged: the exact SA public-sector screening interval/algorithm (HPV-DNA primary versus cytology) is in transition under BetterGyn 2024 / DiaVACCS and should be confirmed against the current PDF before quoting specific intervals; this chapter cites the policy direction, not exact numbers.