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Lupus vs. Hashimoto’s ANA Test Results: What’s Different?

Medically reviewed by Sarika Chaudhari, M.D., Ph.D.
Written by Emily Wagner, M.S.
Updated on September 29, 2026

Key Takeaways

  • Antinuclear antibody (ANA) testing is a common tool used by doctors to help narrow down the cause of symptoms that may point to autoimmune conditions like lupus or Hashimoto's disease, but a positive result alone cannot confirm any specific diagnosis.
  • In lupus, more than 95 percent of people test positive for ANA, yet only a small portion of those with a positive result actually have the condition, meaning doctors rely on additional blood tests, urine tests, and a review of symptoms to make a diagnosis. For Hashimoto's disease, ANA levels may not always be elevated, and doctors often look for other specific thyroid-related antibodies along with hormone levels and imaging to understand what is going on.
  • If you have received a positive ANA test or are experiencing symptoms that concern you, it is a good idea to follow up with your doctor so they can review your full health history, order any additional tests that may be needed, and help you understand what your results mean for your overall health.
  • View all takeaways

Looking at a long list of laboratory tests can feel like trying to decode a different language. Antinuclear antibody (ANA) testing is commonly used to narrow down potential diagnoses — especially for autoimmune diseases like lupus and Hashimoto’s disease.

While ANA tests are part of the diagnostic journey, they can’t confirm any specific health condition. Keep reading to learn more about how ANA testing differs between lupus and Hashimoto’s disease and how doctors use symptoms and other tests to diagnose these conditions.

What Is an ANA Test?

An ANA test measures specific immune proteins (antinuclear antibodies) in your blood. Your immune system makes antibodies to protect you against infections and foreign substances.

🗳️ Have you had an ANA test while being evaluated for lupus or Hashimoto’s disease?
Yes, I’ve had an ANA test.
No, I haven’t had an ANA test.
I’m not sure.

Autoantibodies mistakenly target your body’s own cells and tissues. Antinuclear antibodies specifically attack the nucleus inside your cells. The nucleus holds DNA and proteins.

Many people without any autoimmune disease can have some antinuclear antibodies in their bloodstream. This is because other factors can also trigger your immune system to make ANA, such as:

  • Cancer
  • Viral infections
  • Certain medications

According to a study in the journal Reumatologia, ANAs can also be present in the blood of some healthy people, especially women and older people. However, high ANA levels can point to health problems, like autoimmune diseases. A positive ANA test is only the first step, though. By itself, it can’t diagnose a specific health condition. You need other tests to find out what’s happening.

Autoimmune diseases that cause ANA positivity include:

  • Systemic lupus erythematosus (SLE) or lupus
  • Autoimmune thyroid diseases, like Hashimoto’s disease
  • Sjögren’s disease
  • Rheumatoid arthritis

ANA Test for Lupus

An ANA test may be the first step in diagnosing SLE. Over 95 percent of people with lupus have a positive ANA test. However, only 11 percent to 13 percent of those who do test positive actually have lupus. This means doctors need other tests to make an official lupus diagnosis.

Since most people with lupus have a positive ANA test, a negative test can help rule out the diagnosis. However, you can still have lupus without antinuclear antibodies.

ANA Test for Hashimoto’s Disease

In Hashimoto’s disease, your immune system creates proteins known as autoantibodies that target your thyroid tissue, causing it to attack your thyroid. This causes inflammation and damages your thyroid.

People with Hashimoto’s disease can also have a positive ANA test. A study of 154 people with autoimmune thyroid disease showed that 17.5 percent of people were positive for ANAs, while in another study 35 percent had positive ANAs. One small study of 32 people with Hashimoto’s thyroiditis showed that 47 percent had positive ANAs.

Higher levels of other autoantibodies against thyroid tissue mean that you’re more likely to have antinuclear antibodies too. Examples of these autoantibodies include:

  • Antithyroid peroxidase (anti-TPO) — Targets thyroid peroxidase, an enzyme the thyroid uses to make hormones
  • Anti-thyroid-stimulating hormone (anti-TSH) receptor antibodies — Target the thyroid-stimulating hormone (TSH) receptors
  • Antithyroglobulin (anti-Tg) — Targets thyroglobulin, a protein found in the thyroid

Hashimoto’s disease doesn’t always cause high ANA. Instead, people are usually positive for anti-Tg and anti-TPO antibodies.

Tests That Help Identify Lupus

An ANA test is only one part of diagnosing lupus, and an ANA test alone can’t confirm your diagnosis. Your doctor or rheumatologist will look at your symptoms and other test results to confirm whether you have lupus.

Signs and Symptoms of Lupus

Lupus affects everyone differently, and symptoms vary from person to person. Too much inflammation can damage the skin, joints, and kidneys.

If you notice signs of lupus, tell your doctor. Be on the lookout for:

  • A butterfly-shaped rash covering your nose and cheeks
  • Sores in your mouth and nose
  • Fatigue, dizziness, and headaches
  • Fever
  • Joint pain and swelling, especially in the morning
  • Scaly skin rashes on your body
  • Frothy urine
  • Swelling in legs, ankles, and around the eyes

Other Tests for Lupus

If you have a positive ANA test, your doctor or rheumatologist may order urine and blood tests, including:

  • Complete blood count — Measures your blood cell and platelet counts
  • Urinalysis — Shows how well your kidneys are working and checks for infections
  • Erythrocyte sedimentation rate — Looks at how quickly your red blood cells clump together and fall to the bottom of a test tube, which indicates inflammation
  • Complement levels — Measures proteins from the complement system, another part of your immune system, which attacks your tissues in SLE
  • Autoantibody testing — Checks for other antibodies seen in SLE, including antiphospholipid and antidouble-stranded DNA (anti-dsDNA)

Tests That Help Identify Hashimoto’s

Antinuclear antibodies may not be seen in people with Hashimoto’s disease. Remember, you can have an autoimmune disease without a positive ANA test. Instead, your symptoms and other blood tests will help make a diagnosis.

Signs and Symptoms of Hashimoto’s Disease

Most people with Hashimoto’s disease have hypothyroidism, or low levels of thyroid hormones. Without enough hormones, your body can’t function normally. In rare cases, Hashimoto’s thyroiditis may cause hyperthyroidism, or high levels of thyroid hormones.

It can be hard to diagnose Hashimoto’s at first because many people don’t have any symptoms. As your thyroid hormone levels keep falling, you may notice:

  • An enlarged thyroid gland or a goiter, which can make your neck look and feel swollen
  • Extreme tiredness or fatigue
  • Dry skin
  • Weight gain
  • Hair loss
  • Constipation
  • Slow heart rate
  • Cold intolerance
  • Trouble with memory or concentration
  • Puffy face and eyes
  • Muscle aches and pains
  • Joint pain and stiffness

Other Tests for Hashimoto’s Disease

If you have symptoms of Hashimoto’s disease, your doctor will likely order blood tests. These tests usually confirm whether you have the disease.

Some blood tests look for autoantibodies seen in Hashimoto’s disease, such as anti-TPO, anti-Tg, and anti-TSH receptor autoantibodies.

Because Hashimoto’s damages the thyroid gland, your hormone levels change. High TSH and low thyroxine (T4) levels often point to hypothyroidism. This is because the brain signals to the thyroid to make more TSH. However, the damaged thyroid can’t use TSH to make more T4, the main thyroid hormone.

An enlarged thyroid can be a sign of Hashimoto’s disease — but other conditions can affect its size. An ultrasound takes pictures of the thyroid gland to find out why it may be abnormally large. Thyroid nodules, or small bumps in the tissue, can also cause a goiter.

When a Positive ANA Test Needs Further Evaluation

Getting a positive ANA test can be alarming, and it can leave you wondering what’s next for your health. Remember, some people have antinuclear antibodies in their blood, even if they don’t have an autoimmune disease.

It’s a good idea to follow up with your doctor if you have high ANA levels and signs of an autoimmune disease. They can run more tests for lupus or other autoimmune conditions to rule out potential causes.

The sooner you get the right diagnosis, the better you can treat inflammation and prevent lasting damage. Lupus and Hashimoto’s disease have different treatment plans to control your symptoms and protect your body.

Talk to Your Doctor About Your ANA Test Results

If you recently had an ANA test and want to learn more about your results, talk to your doctor. It’s best not to try to interpret the results yourself — they can be confusing, and you may come to the wrong conclusion.

There’s plenty of information available on the internet, but your doctor knows your health history best. They can help you better understand your ANA test results in the context of your own health.

References
  1. ANA (Antinuclear Antibody) Test — MedlinePlus
  2. Antibodies — Cleveland Clinic
  3. Antinuclear Antibodies (ANA) — American College of Rheumatology
  4. I Have Symptoms of Lupus, but a Negative ANA Test. Can I Still Have Lupus? — Lupus Foundation of America
  5. Hashimoto’s Disease — National Institute of Diabetes and Digestive and Kidney Diseases
  6. Association Between Anti-Nuclear Antibody (ANA) Positivity and Autoimmune Thyroid Disease Markers in a General Examination Population — Biochemistry and Biophysics Reports
  7. Thyroid Peroxidase Antibody Test: What Is It? — Mayo Clinic
  8. Thyroid Antibodies Explained — British Thyroid Foundation
  9. Top 10 Points Lupus Patients Should Know About Autoimmune Thyroid Diseases — Hospital for Special Surgery
  10. Systemic Lupus Erythematosus (Lupus): Diagnosis, Treatment, and Steps To Take — National Institute of Arthritis and Musculoskeletal and Skin Diseases
  11. Lupus Blood Test Results Explained — Hospital for Special Surgery
  12. Hashimoto’s Disease — Mayo Clinic
  13. Rheumatic Disease Autoantibodies in Patients With Autoimmune Thyroid Diseases — Medical Principles and Practice
  14. Presence of Systemic Autoimmune Disorders in Patients With Autoimmune Thyroid Diseases — Annals of the Rheumatic Diseases
  15. Antinuclear Antibodies in Healthy People and Non-Rheumatic Diseases: Diagnostic and Clinical Implications — Rheumatologia
  16. Hashimoto’s Thyroiditis and Autoimmunity Parameters: Descriptive Study — Minerva Medica
  17. Systemic Lupus Erythematosus (Lupus) — National Institute of Arthritis and Musculoskeletal and Skin Diseases
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A MyLupusTeam Member

I have hashimotos and have mixed connective tissue disease (possibly lupus sle). My ANA was 1:320 and specked! In addition I have rashes, recurrent miscarriages and have arthritis! I find all this so… read more

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My ANA test came back negative, but I have every symptom for lupus ,even she said before test I have auto immune. How can I be negative

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