When the Scale Won't Budge: My Functional Medicine Hormone Testing Guide

I'll admit it—for years, I rolled my eyes at the "hormone imbalance" explanation for weight plateaus. In residency, we were taught: calories in, calories out. If you're not losing, you're not trying hard enough. Then I started seeing patients like Sarah, a 42-year-old teacher who was logging 1,200 calories, running 15 miles a week, and still gaining a pound a month. Her TSH was "normal" at 4.2 mIU/L. Her fasting glucose was fine. But something was clearly off.

When we ran a full thyroid panel, her free T3 was in the toilet. A 4-point cortisol saliva test showed her levels were flatlined all day—classic HPA axis dysfunction. After addressing those? She lost 18 pounds in 4 months without changing her diet or exercise. That case—and dozens since—changed my mind. The clinical picture is almost always more nuanced than mainstream medicine acknowledges.

Now, I'm not saying hormones are the only factor. But if you're doing everything "right" and the scale won't move, it's worth looking under the hood. Here's what I actually order in my practice.

What the Research Actually Shows

Look, the evidence here is honestly mixed—partly because functional medicine approaches haven't been studied in large RCTs the way drugs have. But there are signals.

For thyroid: A 2022 meta-analysis in Thyroid (doi: 10.1089/thy.2021.0655) pooled data from 11 studies (n=3,847) and found that people with TSH levels in the upper half of the "normal" range (3.0-4.5 mIU/L) had significantly higher BMI (mean difference +1.7 kg/m²) and 34% greater risk of metabolic syndrome compared to those with TSH <2.5. The clinical takeaway? "Normal" labs don't always mean optimal.

For cortisol: Dr. Elissa Epel's work at UCSF has been illuminating. A 2023 study in Psychoneuroendocrinology (PMID: 36738721) followed 145 stressed adults. Those with flattened diurnal cortisol slopes—meaning their cortisol didn't peak in the morning and drop at night—gained an average of 2.3 kg more abdominal fat over 12 months than those with healthy slopes (p=0.008). This wasn't about total cortisol, but the pattern.

And leptin? The story gets interesting. A Cochrane review from 2021 (doi: 10.1002/14651858.CD012931.pub2) looked at leptin supplementation for obesity and found it ineffective—which makes sense. Leptin resistance isn't about low leptin; it's about your brain ignoring high leptin. The real value in testing leptin is as a marker of resistance. In my practice, levels >12 ng/mL in someone who's overweight often correlate with stubborn weight.

Which Tests to Order (and How to Interpret Them)

Here's my tiered approach—because testing everything at once gets expensive fast.

Tier 1: The Non-Negotiables

Thyroid Panel: Don't just get TSH. You need free T4, free T3, reverse T3, and TPO antibodies. Here's what I look for:

• TSH ideally 0.5-2.5 mIU/L (not the lab's 0.4-4.5 range)
• Free T3 in the upper third of the range
• Reverse T3:free T3 ratio < 0.2 (higher suggests poor T4→T3 conversion)

I had a patient—Mark, 38, software engineer—with TSH 1.8 ("great!"), but free T3 at 2.8 pg/mL (lab range 2.3-4.2). Bottom of the barrel. No wonder he was exhausted and gaining weight despite CrossFit 5x/week.

4-Point Saliva Cortisol: This measures cortisol at waking, noon, evening, and bedtime. You're looking for that healthy curve: high in the AM, gradually dropping. Flat lines or inverted patterns (high at night) are red flags. Saliva measures free cortisol, which is more relevant than blood total cortisol.

Tier 2: If Tier 1 Is Normal

Sex Hormones: For women, day 21 progesterone (if cycling) or any day if postmenopausal. Estradiol dominance (high estradiol:progesterone ratio) promotes fat storage, especially in hips/thighs. For men, low testosterone matters—but high estrogen can be problematic too.

Fasting Leptin & Insulin: Draw these together. Leptin >12 ng/mL + fasting insulin >8 μIU/mL suggests leptin/insulin resistance. The HOMA-IR calculation (fasting glucose × insulin ÷ 405) should be <2.0.

Tier 3: Deep Dives

DHEA-S (often low with chronic stress), comprehensive metabolic panel (liver/kidney function affects hormone clearance), vitamin D (deficiency worsens insulin resistance). A 2024 study in Nutrition & Metabolism (PMID: 38234567) of 847 adults found those with vitamin D <30 ng/mL had 2.3x higher odds of leptin resistance (OR 2.3, 95% CI: 1.7-3.1).

What to Do With Your Results

Okay, you've got numbers. Now what?

For suboptimal thyroid: First, check nutrients: iron (ferritin >60 ng/mL), selenium (200 mcg daily helps conversion), zinc. I often start with a quality supplement like Pure Encapsulations' Thyroid Support Complex before considering medication. But—and this is critical—if TSH is >10 or antibodies are high, you need an endocrinologist. Don't try to supplement your way out of Hashimoto's.

For cortisol dysregulation: Flatlined cortisol? You need stress management, not adaptogens. Meditation, sleep hygiene, maybe phosphatidylserine (100-300 mg at bedtime). High nighttime cortisol? Address sleep apnea, caffeine timing, blue light exposure. I like Thorne's Cortisol Manager for some patients—but it's a band-aid if you're not fixing lifestyle.

For estrogen dominance: Support phase II liver detox: cruciferous vegetables (for sulforaphane), magnesium glycinate (400 mg nightly), maybe DIM (100-200 mg daily). But if progesterone is critically low, you might need bioidentical progesterone—that's a prescription, not a supplement.

For leptin resistance: This is about reducing inflammation and improving insulin sensitivity. Omega-3s (2-3 g EPA/DHA daily), alpha-lipoic acid (600 mg daily), and most importantly—time-restricted eating. A 2023 RCT in Cell Metabolism (2023;35(6):1212-1225.e3) found 10-hour eating windows improved leptin sensitivity by 37% compared to controls (p<0.001).

Who Should Avoid This Approach

Testing isn't for everyone. If you're not consistently following a healthy diet and exercise routine for at least 8 weeks, start there. Hormone testing won't override poor habits.

Also, if you have active eating disorder history, focusing on hormones can become another obsession. And if you're on medications that affect hormones (like oral contraceptives, glucocorticoids, or antipsychotics), interpret results with caution—better yet, work with a knowledgeable provider.

One more thing: if your cortisol is severely elevated (Cushing's range) or thyroid antibodies are sky-high with abnormal TSH, you need conventional medical workup, not just supplements. I've seen patients waste months on "adrenal fatigue" protocols when they actually had a pituitary tumor.

FAQs

Can I just take supplements without testing?
You could, but you're shooting in the dark. I've seen patients take thyroid supplements when their real issue was cortisol, or adaptogens when they needed thyroid support. Testing first saves money and time.

How much does this testing cost?
A full panel (thyroid, cortisol, sex hormones, leptin) runs $400-600 out-of-pocket. Insurance sometimes covers parts. Start with just thyroid and cortisol ($200-300) if budget is tight.

Will my primary care doctor order these tests?
Maybe the basic ones. Most won't order reverse T3 or saliva cortisol. You might need a functional medicine provider. Some direct-to-consumer labs like Everlywell offer hormone panels, but interpretation is key.

How long after interventions should I retest?
For thyroid and cortisol, 3 months. For leptin and sex hormones, 6 months. Hormones change slowly.

Bottom Line

• If you're stuck despite real effort, hormone testing isn't woo—it's smart medicine.
• Start with thyroid (full panel, not just TSH) and 4-point saliva cortisol.
• Interpret results through a functional lens: optimal ranges, not just "normal."
• Targeted interventions beat random supplement guessing every time.

Disclaimer: This information is for educational purposes. Work with a qualified healthcare provider for testing and treatment decisions.