What are the causes of secondary amenorrhea in a female patient of reproductive age?

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Causes of Secondary Amenorrhea

Most Common Etiologies

Secondary amenorrhea in reproductive-age women is most commonly caused by four primary conditions: Polycystic Ovary Syndrome (PCOS), Functional Hypothalamic Amenorrhea (FHA), hyperprolactinemia, and Primary Ovarian Insufficiency (POI). 1

Functional Hypothalamic Amenorrhea (FHA)

  • FHA accounts for 20-35% of secondary amenorrhea cases and represents a functional decrease in pulsatile GnRH secretion leading to decreased LH pulses. 1, 2

  • Key triggering factors include:

    • Stress and increased stress sensitivity 2
    • Vigorous exercise patterns (particularly >10 hours/week of intense training) 3
    • Weight loss and low BMI 2
    • Caloric restriction or energy deficit (<30 kcal/kg fat-free mass/day) 3
    • Psychological disorders 2
  • Laboratory findings show low or normal FSH and LH levels, with a negative progestin challenge test. 2

  • Critical complication: Patients face 2-fold increased fracture risk and decreased bone density, requiring DXA scan if amenorrhea extends beyond 6 months. 3

Polycystic Ovary Syndrome (PCOS)

  • PCOS is one of the most common causes of secondary amenorrhea, characterized by polycystic ovarian morphology on ultrasound. 1, 2

  • Laboratory findings include LH:FSH ratio >2, which strongly suggests PCOS. 2

  • Patients require screening for glucose intolerance, dyslipidemia, and metabolic syndrome. 4

  • Important diagnostic pitfall: FHA-PCOM affects 40-47% of women with FHA and can be misdiagnosed as PCOS because these patients fulfill Rotterdam criteria despite having functional hypothalamic amenorrhea with polycystic ovarian morphology. 1, 2

Hyperprolactinemia

  • Hyperprolactinemia accounts for approximately 20% of secondary amenorrhea cases. 1, 2

  • Clinical presentation may include galactorrhea, though this is not always present. 2

  • Laboratory findings show elevated serum prolactin levels, and patients may require pituitary imaging to exclude adenoma. 2

  • In women with epilepsy, functional hyperprolactinemia occurs at increased rates due to postictal prolactin elevations and interictal epileptic activity propagated to the hypothalamus. 5

Primary Ovarian Insufficiency (POI)

  • POI is characterized by elevated FSH and LH levels in the menopausal range in women under age 40. 1, 2

  • Critical point: Patients with POI can maintain unpredictable ovarian function and should not be presumed infertile. 1, 4

  • Hormone replacement therapy is indicated to reduce risk of osteoporosis, cardiovascular disease, and urogenital atrophy. 3

Additional Important Causes

Thyroid Dysfunction

  • Both hypothyroidism and hyperthyroidism can cause secondary amenorrhea, identified by abnormal TSH levels. 2

Advanced Liver Disease

  • In women with advanced liver disease, altered estrogen metabolism and disruption of the hypothalamic-pituitary axis with low FSH and LH can lead to anovulation and amenorrhea. 5

  • Amenorrhea or oligomenorrhea occurs in more than 25% of women with advanced liver disease and nearly 75% of premenopausal women awaiting liver transplant. 5

  • Excess alcohol intake directly affects the hypothalamic-pituitary axis and ovarian function. 5

Epilepsy-Related Causes

  • Women with temporal lobe epilepsy have a 12% rate of hypothalamic amenorrhea (hypogonadotropic hypogonadism) compared to 1.5% in the general population. 5, 1

  • Antiepileptic drugs (carbamazepine, phenobarbital, phenytoin) induce hepatic cytochrome P450-dependent steroid hormone breakdown and SHBG production, reducing biologically active sex hormone concentrations. 5

  • Women with epilepsy face increased risk of premature menopause, with 4% experiencing primary gonadal failure in their third decade versus 1% expected in the general population. 5

Diagnostic Approach Algorithm

First-Line Evaluation

  • Pregnancy test is mandatory as the first step in all cases of secondary amenorrhea. 2, 3

  • Initial laboratory panel must include serum FSH, LH, prolactin, and TSH levels. 1, 2, 3

  • Pelvic ultrasound should be performed to evaluate for polycystic ovarian morphology and uterine abnormalities. 2, 3

Interpretation of Initial Results

  • Low/normal FSH and LH with negative progestin challenge → FHA 2

  • LH:FSH ratio >2 with polycystic ovaries → PCOS 2

  • Elevated FSH and LH → POI 2

  • Elevated prolactin → Hyperprolactinemia (obtain pituitary imaging) 2

  • Abnormal TSH → Thyroid dysfunction 2

Additional Testing When Indicated

  • Androgen profile for suspected PCOS or signs of hyperandrogenism 2

  • Progestin challenge test to determine estrogen status 2, 3

  • Energy availability calculation (>30 kcal/kg fat-free mass/day) for suspected FHA 3

  • DXA scan for bone mineral density if amenorrhea extends beyond 6 months 3

Critical Diagnostic Pitfalls

FHA-PCOM Misdiagnosis

  • FHA-PCOM patients have polycystic ovarian morphology but require completely different treatment than PCOS. 1, 2

  • Distinguish FHA-PCOM from PCOS by:

    • Clear history of FHA triggers (energy deficit, excessive exercise, stress) 1
    • Negative progestin challenge test indicating low estrogen 1
    • Lower LH levels (not elevated LH:FSH ratio) 1
    • Higher SHBG levels compared to PCOS 1
    • Lean body type with low or normal BMI 2
  • Treatment for FHA-PCOM requires correction of energy deficit, not PCOS-directed therapy. 2

Common Clinical Errors to Avoid

  • Do not prescribe oral contraceptives as first-line therapy for FHA, as this masks the problem without addressing the underlying energy deficit and does not protect bone mineral density as effectively as physiologic estrogen replacement. 3

  • Do not assume amenorrhea in athletes or stressed patients is benign – other pathology must be excluded even when clinical picture suggests FHA. 3

  • Do not overlook eating disorders, as patients frequently minimize or deny disordered eating behaviors requiring direct questioning about specific behaviors. 3

  • Do not delay bone density assessment – DXA scanning is indicated regardless of age if amenorrhea extends beyond 6 months. 3

References

Guideline

Causes of Secondary Amenorrhea

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Guideline

Major Causes of Secondary Amenorrhea

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Guideline

Amenorrhea Diagnosis and Management

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2026

Research

Amenorrhea: an approach to diagnosis and management.

American family physician, 2013

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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