How to Properly Interpret Lab Tests for Autoimmune Disease

Still Sick Even When Your Labs Are Normal? Here’s Why

Many autoimmune patients tell me that their doctor has already checked their lab results and everything came back normal. But if that’s the case, why are they still feeling sick? It just doesn’t add up, right?

The reality is that when I repeat tests or order additional ones, the results often aren’t as normal as they seemed, especially from a functional medicine perspective. So why does this happen?

The key difference is that conventional medicine tends to focus on standard lab tests designed to make a diagnosis that’s easy for other doctors to understand. These tests serve to label things, but they often don’t address or pinpoint the underlying causes of a patient’s symptoms. That’s why even if a patient’s tests come back “normal,” there might still be crucial information missing. Let’s break down why this happens.

Is Your Doctor Running the Right Tests?

One of the first questions to ask is whether your doctor is using the correct tests to get a complete picture of your health. Are they running enough tests to really understand what’s going on? And are they using the right type of specimen for each test?

Another big factor is how the lab results are interpreted. Are your doctor’s conclusions based on standard reference ranges, or are they looking at optimal lab ranges that are more aligned with health, not just “normal” numbers?

If you’re wondering, “Can blood tests be wrong?” or “Are blood tests accurate?” the answer depends on how the tests are interpreted and whether you’re getting the right ones.

What Routine Blood Tests Can (And Can’t) Detect

In the past, doctors ordered a wide variety of tests—around 25 to 27 panels. But now, standard blood tests are often limited to just 5 panels, typically including a complete blood count (CBC), comprehensive metabolic panel (CMP), thyroid-stimulating hormone (TSH), lipid panel, and sometimes a hemoglobin A1c (HbA1c) to track blood sugar levels.

The question is, did your doctor run enough tests to get a full picture of your health? When you hear that your labs are normal, it’s worth asking, “What exactly did they test for?” There might be other factors that were missed.

Thyroid Testing

When doctors check your thyroid, they usually only test for TSH (thyroid-stimulating hormone). But TSH alone doesn’t give a complete picture of thyroid health. There are 11 markers that should be assessed to understand thyroid function fully. As a functional medicine practitioner, I look at all the relevant thyroid markers and focus on what’s optimal, not just what’s “within range.”

Blood Sugar Testing

Many doctors focus on blood sugar levels but ignore insulin testing, which is just as important. Even if your HbA1c or fasting glucose levels are normal, you might have hidden insulin resistance. This means the doctor might miss a key aspect of your health.

Vitamin D

Vitamin D deficiency is common in autoimmune patients, but many don’t even get tested for it. Since insurance doesn’t always cover vitamin D testing, many doctors don’t see it as a priority. However, low vitamin D levels can be a crucial piece of the puzzle, especially for those with autoimmune conditions.

C-Reactive Protein (CRP) and Homocysteine

High-sensitivity CRP (hs-CRP) and homocysteine are inflammation markers, and they also serve as cardiovascular risk markers. Unfortunately, these tests aren’t often ordered unless you’ve already experienced a heart attack or stroke. But why wait for a problem to occur when you could prevent it with early testing?

Is a Blood Test for Cortisol Accurate?

Stress plays a huge role in autoimmune diseases, which is why cortisol testing can be useful. However, blood tests for cortisol aren’t the most accurate because the stress of having blood drawn can elevate cortisol levels temporarily. For a more accurate picture, salivary cortisol testing is better, as it checks cortisol levels throughout the day, revealing how your body is responding to stress over time.

Gut Testing

When it comes to gut health, doctors often rely on tests like colonoscopies or stool tests to check for blood or infections. However, these tests may miss signs of an inflamed or leaky gut, food sensitivities, or imbalances in gut bacteria. Even standard stool tests focus mainly on pathogens, but don’t check for the health of your gut microbiome or markers of inflammation. A more comprehensive gut test can reveal a lot more about your digestion and overall health.

Food Sensitivity Testing

Routine food sensitivity tests can often miss the mark. Standard food allergy tests (like the IgE panel) detect only immediate allergic reactions, but they won’t identify sensitivities or intolerances. An IgG test might be used, but that only covers part of the picture. Testing for food sensitivities is more complex and may require multiple tests to get accurate results.

Different Specimen Types Matter

Different types of specimens—blood, saliva, urine—are used depending on what’s being tested. For example, when it comes to hormones, saliva tests are often better than blood tests for understanding how much active hormone is available in your body. Urine tests can be helpful for tracking how your body is metabolizing hormones, like estrogen. Knowing which test to use for what you’re looking for is key to getting accurate results.

Timing Matters

Lab tests give you a snapshot of your body’s state at a particular moment in time. For instance, blood sugar levels can vary depending on the time of day, so a single fasting blood sugar test might not tell you the full story. Continuous glucose monitors can give a better picture by tracking blood sugar throughout the day.

Getting the right tests, at the right time, and interpreting the results correctly is crucial for understanding your autoimmune condition and overall health. If you’re feeling unwell, even with “normal” lab results, it might be time to ask for a more comprehensive evaluation.