Amenorrhea and Chronic Illness: Causes, Risks, Tests, and Treatment

When periods stop, most people get told it’s “stress” or “weight.” Sometimes that’s true. But missed periods are often your body’s early-warning light for chronic illness. If you’ve had no bleeding for months, you’re not only wondering why-you’re wondering what to do next and whether your bones or fertility are at risk. I’m writing this from windy Wellington with a Border Collie at my feet and a Siamese stalking the keyboard, and here’s the clear, no-fluff guide I wish more people got in clinic.

• TL;DR: Missing periods (secondary amenorrhea) often tie back to chronic conditions like PCOS, thyroid disease, high prolactin, celiac disease, diabetes, inflammatory bowel disease, chronic kidney disease, or the meds used to treat them.
• When to act: If you miss three periods in a row, had irregular cycles for six months, or never started by age 15-16, book a medical review. Always rule out pregnancy first.
• What to expect: Your clinician will check pregnancy, thyroid, prolactin, ovarian hormones, sometimes celiac antibodies, and may image your pelvis or pituitary.
• Why it matters: Months without estrogen can lead to bone loss, mood changes, vaginal dryness, and fertility issues-most are reversible when treated early.
• Fixable: Treat the root condition, adjust meds, and use targeted hormones or lifestyle changes. Many people restart cycles and protect bone and heart health.

Why periods stop when you’re unwell: the science and the culprits

Your cycle depends on a small but sensitive circuit called the HPO axis-the hypothalamus, pituitary, and ovaries talking in tiny hormone pulses. Chronic illness can jam that conversation in a few repeatable ways:

• Stress signals and inflammation blunt the brain’s hormone pulses (hypothalamic suppression).
• Endocrine issues miswire the feedback loop (PCOS, thyroid disorders, high prolactin).
• Nutrient malabsorption or energy deficit deprive the brain and ovaries (celiac, IBD, severe dieting, endurance training).
• Organ disease shifts hormone metabolism (kidney, liver), and some drugs directly shut ovulation (antipsychotics, chemo, opioids).

A quick map of common links:

• PCOS: The most common cause of persistent irregular or absent periods in reproductive-age people. Often shows up with acne, scalp hair thinning, or excess facial/body hair. Insulin resistance is a major driver.
• Thyroid disease: Both low and high thyroid function can stop ovulation. Fatigue, heat/cold intolerance, weight changes, and constipation/diarrhea are clues.
• Hyperprolactinemia: High prolactin from a pituitary microadenoma, meds like risperidone, or chest wall stimulation can suppress ovarian hormones.
• Celiac disease and IBD: Inflammation plus poor nutrient absorption can silence cycles, even without dramatic weight loss.
• Diabetes: Fluctuating blood sugars and insulin resistance affect ovulation; poor control correlates with menstrual issues.
• Chronic kidney or liver disease: Alter hormone carriers and metabolism, disturbing the cycle.
• Functional hypothalamic amenorrhea (FHA): Energy deficit from low intake, high output, illness, or psychological stress causes the brain to downshift reproduction to conserve energy.

Why you shouldn’t wait: After about six months without estrogen exposure, bone turnover goes the wrong way. The Endocrine Society notes bone loss can start within months with FHA and hypogonadism. ACOG and bpacnz (NZ primary care guidance) advise assessment if three cycles are missed or if periods never begin by mid-teens.

What’s “normal to miss”? If you recently changed contraception, gave birth, or are perimenopausal, some irregularity can be expected. But persisting absence still deserves a check.

Evidence touchpoints: ACOG’s Amenorrhea guidance (2023-2024 updates), Endocrine Society guidelines on functional hypothalamic amenorrhea (2017) and hyperprolactinemia (2011; reaffirmed), international PCOS guideline (2018, updated 2023), and WHO definitions standardize the workup and thresholds to act.

What to do now: step-by-step plan, decision rules, and checklists

Here’s a simple, practical plan you can take into a GP appointment-works in New Zealand and beyond.

1. Rule out pregnancy today. Use a home urine test; if negative and still no bleed in a week, repeat or get a blood hCG.
2. Check your timeline. If you’ve missed three periods in a row (or had irregular cycles for six months), book a medical review. Teens who haven’t started periods by 15-16 or within three years of breast development also need an assessment.
3. Gather your history. Write down: last period date, typical cycle length, past patterns, weight changes, new meds, illnesses, stress, training volume, and any nipple discharge or headaches.
4. Book labs and a visit. Ask for: hCG, TSH with reflex free T4, prolactin (avoid nipple stimulation before test), FSH/LH and estradiol, and total/free testosterone plus SHBG if PCOS signs present. Consider celiac antibodies (tTG-IgA) if GI symptoms, iron or B12 deficiency, or family history. HbA1c and fasting lipids if PCOS or diabetes risk.
5. Discuss imaging. Pelvic ultrasound if PCOS or structural concerns. Pituitary MRI if prolactin is persistently high or neurological symptoms.
6. Protect bones if amenorrhea persists. Ask about calcium/vitamin D, resistance training, and whether you need a bone density scan (DEXA) after six months of hypothalamic amenorrhea or longer with other causes.
7. Co-create a treatment plan. This may include managing the chronic condition, nutrition changes, cognitive behavioral therapy for stress, metformin for PCOS/insulin resistance, thyroid hormone replacement, dopamine agonists for hyperprolactinemia, or temporary hormonal therapy to protect the endometrium and bones.

Quick decision rules (not a diagnosis, but good navigation):

• 3-by-3 rule: Three missed cycles if you used to be regular → see your clinician.
• Red flags: Severe headaches with visual changes, galactorrhea (milk-like discharge not postpartum), hot flashes/night sweats under 40, pelvic pain or unexpected bleeding, unexplained weight loss, or signs of eating disorder → urgent review.
• Med check: Start of antipsychotics, opioids, chemo, or high-dose steroids coinciding with missed periods → discuss alternatives or add-back therapy.

What to bring to your appointment:

• A cycle log (calendar dates or app screenshots).
• List of all meds and supplements, including doses.
• Family history of thyroid disease, PCOS, diabetes, early menopause, celiac disease.
• Training schedule, recent changes in diet or weight.
• Your top three goals (restart periods, protect fertility, fix fatigue, etc.).

Common pitfalls to avoid:

• Assuming “it’s just stress” for months without testing.
• Relying on cycle apps that predict periods even when ovulation isn’t happening.
• Skipping bone health when periods have been absent more than six months.
• Stopping meds cold turkey to restart periods-always talk to your prescriber first.

Conditions at a glance: mechanisms, signs, tests, and treatments

This table sums up the most frequent chronic drivers of missed periods and what usually happens next in clinic. It’s meant for quick orientation-you and your clinician will tailor it.

Notes:

• Pelvic ultrasound is helpful but not required to diagnose PCOS in many cases; clinical and lab features can suffice (International PCOS Guideline 2023).
• Estradiol is often low in FHA and hyperprolactinemia; in PCOS, estradiol may be low-normal but ovulation is inconsistent.
• In teens, avoid labeling PCOS too early; cycles can be irregular for the first 1-3 years post-menarche.

Two quick real-world examples:

• Type 1 diabetes in her late 20s with HbA1c 80 mmol/mol, new amenorrhea: Intensive glucose coaching plus a combined pill to regulate bleeding leads to spontaneous cycles returning within months as HbA1c drops to 55.
• Endurance runner with normal BMI but low energy intake: Adding 400-600 kcal/day, dropping one hard session weekly, and getting dietitian support restarts ovulation in 3-6 months; transdermal estradiol is used short-term to protect bone.

Fertility, bones, and long‑term risks: what changes and how to protect yourself

Fertility: If your periods are absent because you’re not ovulating, conception is harder but very often fixable once the underlying issue is treated. PCOS responds well to ovulation induction (letrozole first-line). Hyperprolactinemia often resolves with dopamine agonists. FHA improves with energy repletion and stress work. Thyroid correction can normalize ovulation.

Endometrium: With irregular or absent ovulation, the uterine lining can build up under estrogen without progesterone opposition, especially in PCOS. That can cause heavy bleeding and, over years, increase risk of endometrial hyperplasia. Cyclic progestin or a progestin IUD protects the lining even if you’re not ready for a contraceptive pill.

Bones: Estrogen helps build and maintain bone. Prolonged hypoestrogenism (FHA, hyperprolactinemia, early ovarian insufficiency) can drop bone density fast. Think in months, not years. Rugby players and dancers alike see this. A DEXA scan is reasonable after six months of FHA, sooner if you’ve had stress fractures. Weight-bearing work and adequate calcium (roughly 1000 mg/day, 1300 mg for teens) and vitamin D (per local guidelines) matter, but you also need estrogen restored-naturally or via transdermal estrogen with cyclic progesterone if cycles are not returning.

Mood and cognition: Low estrogen can worsen sleep, anxiety, and concentration. Thyroid imbalance compounds fatigue and mood changes. Addressing the medical driver often lifts these symptoms faster than any supplement.

Cardiometabolic health: In PCOS and diabetes, prioritize insulin resistance and lipids. Waist circumference, blood pressure, fasting lipids, and HbA1c give you a baseline. Small sustainable changes (protein at breakfast, walking after meals, resistance training twice a week) shift insulin sensitivity more than perfect-but-brief diets.

Sexual health: Vaginal dryness and low libido are common with low estrogen. Vaginal moisturizers or local estrogen can help while you fix the root cause. If intercourse is painful, ask for options-there are many.

FAQ and next steps for different scenarios

Mini‑FAQ

• I’m on the pill and don’t bleed on the sugar pills-is that amenorrhea? No. That’s a withdrawal bleed pattern controlled by the pill. True amenorrhea is absence of spontaneous periods off hormones. If you stop the pill for three months and still don’t bleed, then evaluate.
• Can I be pregnant without periods? Yes. Always test if there’s any chance of pregnancy, even if you think you didn’t ovulate.
• Do I need an ultrasound first? Not always. Doctors often start with blood tests. Ultrasound is helpful when PCOS or structural concerns are likely.
• Is metformin a weight-loss drug? No. It improves insulin sensitivity. In PCOS, it can help cycles and metabolic markers; any weight change is usually modest.
• How long to wait for cycles to restart? With FHA, expect 3-6 months after restoring energy balance. Thyroid and prolactin causes can normalize within weeks to a few months once treated.
• Can strength training hurt fertility? No. Smart, progressive resistance work supports hormones and bone health. The risk comes from under-fueling, not lifting.

Scenario‑based next steps

• Teen with no period by 16: See your GP. They’ll review puberty milestones, run basic labs, and consider genetic or structural causes if development is delayed. Avoid quick PCOS labels in early adolescence.
• Athlete with 10+ hours/week training: Track energy intake for two weeks. If you’re missing periods, aim to add 300-600 kcal/day and swap one high-intensity session for mobility/strength. Reassess in six weeks.
• Trying to conceive: Ask about letrozole if PCOS. For FHA, fertility follows energy restoration; a reproductive endocrinologist can discuss short-term induction if needed.
• On antipsychotics with missed periods: Don’t stop meds on your own. Ask your prescriber about options with less prolactin effect or add-back strategies to protect bones and the endometrium.
• Thyroid symptoms and missed periods: Request TSH and free T4. Treating hypo/hyperthyroidism often restarts ovulation without further fertility drugs.
• In New Zealand: A GP can order the initial panel and ultrasound. If prolactin is high or cycles don’t return with first-line care, referral to endocrinology or gynecology is standard through the public system; private care is an option if you want faster imaging.

Cheat‑sheet checklist to print

• Pregnancy test (now and repeat in a week if needed)
• Ask for labs: hCG, TSH, free T4, prolactin, FSH/LH, estradiol, total/free testosterone, SHBG; add tTG‑IgA, HbA1c, lipids if indicated
• Consider ultrasound, MRI (if prolactin high or neuro signs)
• Bone plan: DEXA if ≥6 months amenorrhea with low estrogen, plus resistance training and calcium/vitamin D
• Medication review for prolactin-raising or ovulation-suppressing drugs
• Set a follow-up date (4-8 weeks) to review results and adjust

Professional guidance that shapes this playbook: ACOG Amenorrhea FAQs and Committee Opinions (2023-2024); Endocrine Society Clinical Practice Guidelines on Functional Hypothalamic Amenorrhea (2017) and Hyperprolactinemia; International Evidence‑based Guideline for the Assessment and Management of PCOS (2018; 2023 update); WHO reproductive health definitions; bpacnz primary care guidance on amenorrhoea.

If you’re sitting there thinking, “Maybe it’s just my training ramp-up,” here’s my nudge: get the labs. I’ve seen cycles return fast once the driver is clear and treated. Clarity beats guessing, and your bones will thank you.