Endocrinology

Biopsy and Molecular Testing for Thyroid Nodules

At a Glance

Thyroid nodule biopsy results are grouped by the Bethesda System. Benign or negative molecular results may support ultrasound monitoring, while indeterminate or suspicious results may lead to repeat biopsy, further testing, or surgery; no molecular test alone proves cancer.

If your doctor finds a suspicious nodule on an ultrasound, the next step is often a biopsy to look at the cells directly. This process can be stressful, but understanding what the pathologist (the doctor who studies the cells) is looking for can help you navigate the results.

The Fine-Needle Aspiration (FNA) Biopsy

A Fine-Needle Aspiration (FNA) is the standard way to sample thyroid tissue. It is a quick, outpatient procedure that is generally very safe, with a complication rate of around 1.1% ^[1].

The Procedure: Using an ultrasound to guide the way, the doctor inserts a very thin needle (thinner than the one used to draw blood) into the nodule ^[2]. They usually make 2 to 3 “passes” to ensure they get enough cells for a clear reading ^[3].
What to Expect: You will be awake, and the area may be numbed with a local anesthetic. The most common side effect is minor bruising or a small hematoma (a collection of blood under the skin), which occurs in fewer than 1% of cases ^[4].
The Goal: The goal is to obtain a “diagnostic” sample—enough clear cells for the pathologist to classify using the Bethesda System.

Understanding the Bethesda System

Pathologists use a standardized ranking system called the Bethesda System to describe the risk of cancer in a nodule. The system was updated in 2023 to refine these risk estimates. The percentages below are population estimates; your exact risk may vary ^[5].

Category	Name	Meaning	Estimated Risk of Cancer	Usual Next Steps
I	Nondiagnostic	Not enough cells were collected to make a call.	Varies ^[5]	Usually repeat ultrasound-guided FNA.
II	Benign	The cells look normal/non-cancerous.	~2% – 7% ^[5]	Routine ultrasound monitoring.
III	AUS	“Atypia of Undetermined Significance.” Some cells look unusual.	~22% ^[6]	Repeat FNA, molecular testing, or diagnostic surgery.
IV	Follicular Neoplasm	Cells suggest a specific type of growth that needs more investigation.	~30% ^[6]	Molecular testing or diagnostic surgery.
V	Suspicious	Strong evidence the nodule may be malignant (cancerous).	~74% ^[6]	Specialist discussion, usually surgery.
VI	Malignant	The cells are clearly cancerous.	97% – 100% ^[5]	Surgery.

The “Indeterminate” Challenge (Bethesda III and IV)

Categories III and IV are considered indeterminate, meaning the cells don’t look clearly benign, but they don’t look clearly like cancer either ^[6].

This happens most often with nuclear atypia or follicular growths. To tell the difference between a benign follicular nodule and follicular cancer, a doctor must see the outer shell (the capsule) of the nodule to see if the cells have broken through it or into blood vessels ^[7]. A needle biopsy only takes a few cells from the middle, so it cannot see the capsule. In the past, many patients with these results proceeded to “diagnostic surgery” to remove half the thyroid just to get a final answer ^[8].

Molecular Testing: Avoiding Unnecessary Surgery

To help avoid unnecessary surgeries where the nodule turns out to be benign, doctors now frequently use molecular testing (such as Afirma GSC or ThyroSeq v3) ^[9], repeat the biopsy, or sometimes recommend surveillance. These tests look at the DNA and RNA within the cells you already provided during your biopsy.

Rule-Out Power: These tests have a high Negative Predictive Value (NPV), sometimes up to 93% to 99% depending on the specific test and local cancer prevalence ^[10]^[11]. This means if the test comes back “Benign” or “Negative,” it significantly lowers your risk, and you may be able to simply monitor the nodule with ultrasounds instead of having surgery ^[12]^[13].
Risk-Refining: If the test is “Suspicious” or “Positive,” it doesn’t automatically mean you have cancer, but it increases the probability. Some tests can even identify specific high-risk mutations (like BRAF or TERT) that help your doctor decide how aggressive the surgery needs to be ^[11]^[14].

It is important to remember that these tests are tools to help with decision-making, not a final “yes or no” diagnosis. Your doctor will combine these results with your ultrasound features and personal health history to determine the best path forward ^[15].

Common questions in this guide

What happens during a thyroid nodule FNA biopsy?

During a fine-needle aspiration, an ultrasound guides a very thin needle into the thyroid nodule to collect cells. You usually remain awake, may receive a local anesthetic, and the clinician often makes two or three passes. Mild bruising or a small collection of blood under the skin can occur.

What do the Bethesda categories mean on a thyroid biopsy report?

The Bethesda System classifies the sample from nondiagnostic or benign to indeterminate, suspicious, or malignant. Categories III and IV are indeterminate, meaning the cells are not clearly benign or cancerous, while category VI is clearly cancerous. The recommended next step depends on the category and your ultrasound and health history.

What does an indeterminate Bethesda III or IV result mean?

It means some cells look unusual or show a follicular growth pattern, but the biopsy cannot confirm whether the nodule is cancerous. A needle sample cannot show whether cells have broken through the nodule’s outer capsule or into blood vessels. Your doctor may recommend a repeat biopsy, molecular testing, surveillance, or diagnostic surgery.

How can molecular testing help with a thyroid nodule?

Tests such as Afirma GSC and ThyroSeq v3 analyze DNA or RNA from cells collected during the biopsy. A benign or negative result can substantially lower the chance of cancer and may support ultrasound monitoring, while a suspicious or positive result raises concern but does not prove cancer. Your doctor combines the result with the ultrasound and your health history.

Can molecular testing help me avoid thyroid surgery?

Sometimes. When a test indicates a low risk of cancer, your doctor may recommend monitoring instead of diagnostic surgery, depending on the nodule and your overall risk. A higher-risk result may support surgery, but the test is a decision-making tool rather than a final yes-or-no diagnosis.

Curated prompts to bring to your next appointment.

1.What was the exact Bethesda category and subcategory (like 'nuclear atypia') of my biopsy result?
2.If my result is Bethesda III or IV, do you recommend a repeat biopsy or moving straight to molecular testing?
3.Is my nodule a 'Hürthle cell' or 'oncocytic' type, and does that change how we interpret the tests?
4.What is the specific risk of malignancy for this Bethesda category at this hospital?
5.If we do molecular testing, will the results help us decide between monitoring the nodule or having a diagnostic lobectomy?

Tap a prompt to share your answer — we'll use it plus this page's context to start a tailored conversation.

References (15)

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This page explains thyroid nodule biopsy categories and molecular testing for informational purposes only and does not constitute medical advice. Your endocrinologist, pathologist, or surgeon should interpret your results and advise you about monitoring or surgery.

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