What Causes a False Positive Lyme Test?

False positive Lyme disease tests are caused by antibodies your immune system made for something other than the Lyme bacterium, but that happen to react with the test’s target proteins. The most common culprits are other spirochetal infections like syphilis, certain viral infections such as Epstein-Barr virus, and autoimmune conditions like lupus. How often these false positives matter depends heavily on where you live, when the test is performed, and which tier of the standard testing protocol catches the error.

How the Standard Lyme Test Works, in Brief

In the United States and Canada, the recommended approach is a two-step process. First, a screening blood test (usually an enzyme immunoassay) checks whether your blood contains antibodies that react to proteins from Borrelia burgdorferi, the bacterium behind Lyme disease. If that first test comes back positive or borderline, a second, more specific test called a Western blot is run on the same blood sample to confirm the result. The idea is that the first test casts a wide net and the second one filters out the false alarms.

The two-tier system has a specificity above 95% for confirmed Lyme disease, meaning that fewer than 5 out of every 100 people without Lyme will test positive.¹ That sounds reassuring, but 5% is not zero, and in certain situations the rate of false positives on the initial screening test is much higher. It is the screening step that trips people up, because it was designed to be sensitive rather than specific. False positives become a real clinical problem when the screening test is positive, the confirmatory blot is skipped or misread, or the patient’s situation makes cross-reactivity especially likely.

Other Spirochetal Infections

The single best-documented cause of false positive Lyme tests is syphilis. The bacterium that causes syphilis, Treponema pallidum, is a spirochete, the same corkscrew-shaped family of bacteria that includes Borrelia burgdorferi. Because these organisms share structural proteins, antibodies made against one can light up tests designed for the other. Research going back to the late 1980s confirmed that blood from syphilis patients cross-reacted with both the IFA and ELISA screening tests for Lyme disease.² Relapsing fever, caused by a closely related Borrelia species, can cause similar cross-reactions.³

There is also a subtler version of this problem. Treponema-like spirochetes live naturally in the human mouth, especially in people with gum disease. In one study, about a quarter of people with gingivitis or periodontitis tested positive on the Lyme ELISA, despite never having had Lyme disease. When the interfering antibodies were absorbed out using treponeme preparations, the false positivity dropped.⁴ This does not mean everyone with gum disease will get a false positive on a complete two-tier evaluation, but it does mean the initial screening test can be tripped by oral bacteria you never knew you had.

Viral Infections That Mimic Lyme Antibodies

Epstein-Barr virus, the cause of infectious mononucleosis, is one of the more frustrating sources of Lyme test confusion. EBV triggers a broad immune activation that produces antibodies reactive to many different targets, including some Lyme test antigens. This cross-reactivity between Lyme and EBV serologic assays is well documented and can complicate diagnosis in both directions.⁵ The timing makes things worse: mono is common in teenagers and young adults, peaks in spring and summer (when Lyme transmission is also highest), and causes fatigue, joint aches, and swollen lymph nodes that can look a lot like early Lyme disease.

Cytomegalovirus is another viral culprit, and for similar reasons. Both EBV and CMV cause polyclonal B-cell activation, meaning they ramp up antibody production across the board rather than just against themselves. Some of those broadly stimulated antibodies happen to recognize Borrelia proteins.³ If you are being evaluated for fatigue and joint pain, and both a Lyme screening test and an EBV test come back positive, the question of which infection is actually causing your symptoms can become genuinely difficult to untangle.

Autoimmune Conditions and Rheumatoid Factor

Autoimmune diseases are among the most common reasons for misleading Lyme test results, particularly on the first-tier ELISA. In a study of patients with systemic lupus erythematosus, 40% tested positive for Lyme antibodies on ELISA. Among rheumatoid arthritis patients, the figure was 8%, and for those with seronegative arthritis it was 4%. When those same samples were run through the more specific Western blot, however, none of the lupus patients confirmed positive.⁶ The lupus result is a striking example of why the two-tier system exists: the screening test alone would have flagged nearly half of lupus patients as Lyme-positive.

The rheumatoid arthritis picture was more complicated. Over half of RA patients who were ELISA-positive also showed cross-reactivity to multiple Borrelia antigens on immunoblot, which means the confirmatory test did not cleanly sort out all the false positives in that group.⁶ The strongest correlation was with IgM rheumatoid factor, a type of autoantibody that is itself notoriously sticky and promiscuous in binding to test components. Rheumatoid factor has been shown to nonspecifically recognize Borrelia proteins, producing false positives even in the absence of any spirochetal infection.³

What this means practically is that if you have lupus, rheumatoid arthritis, or another autoimmune condition and develop symptoms like fatigue or joint pain, a positive Lyme screening test should be interpreted with extra caution. The confirmatory blot becomes more important, not less, and even it may not fully resolve the ambiguity in some autoimmune patients.

The IgM Problem

Much of the false-positive trouble in Lyme testing centers on IgM antibodies rather than IgG. IgM is the first antibody class your body produces after an infection. It appears early, it is less specific than IgG, and it tends to cross-react with a wider variety of targets. The IgM portion of the Western blot, in particular, has been criticized for being both insensitive and nonspecific in early Lyme disease.⁷

CDC guidelines say IgM criteria should only be applied during the first four weeks of illness, because after that window, IgM positivity alone becomes unreliable. But in practice, not all clinicians follow this rule. When IgM blot results are used to diagnose someone who has had symptoms for months, the chance of a false positive climbs, and this has contributed to misdiagnosis of so-called “chronic Lyme disease” based on a late-applied IgM result that was never truly positive for Lyme in the first place.⁷

Why Geography Changes Everything

Even a highly specific test produces more false positives than true positives when the disease is rare in the population being tested. This is a basic statistical reality that has major implications for Lyme testing. In a retrospective study at a North Carolina medical center, fewer than 20% of patients with positive Lyme test results actually had illnesses consistent with Lyme disease. Of 70 seropositive patients whose records were reviewed, only 12 turned out to have clinically likely Lyme, and six of those had traveled to areas where the disease is common.⁸

In the northeastern United States, upper Midwest, and Pacific coastal areas where Lyme is endemic, a positive test in someone with a tick bite and a rash is very likely to be real. In the Southeast, Southwest, or other low-prevalence regions, the same positive test is far more likely to be a false alarm. A test with 97% specificity still means 3 out of 100 uninfected people test positive. If only 1 in 1,000 people tested in that area actually has Lyme, those 3 false positives outnumber the single true positive by a wide margin. The test did not fail; it was just applied in a setting where its predictive power collapses.

This is why many infectious disease specialists argue that Lyme testing should only be ordered when the clinical picture is already suspicious for Lyme. Ordering the test as a screening tool in someone with vague fatigue in a low-prevalence area is a recipe for false positives and downstream harm, including unnecessary antibiotics and missed diagnoses of the actual problem.

Misdiagnosis and Symptom Overlap

False positives do not exist in a vacuum. They interact with diagnostic expectations. When a patient has fatigue, brain fog, or joint pain and a Lyme test comes back positive, the temptation is to call the case solved. But in a landmark study of 788 patients referred to a Lyme disease clinic, 57% turned out not to have Lyme disease at all. The majority of those patients were ultimately diagnosed with chronic fatigue syndrome or fibromyalgia, with others having unrelated rheumatic or neurological conditions.⁹

A separate study found that 77 patients with symptoms attributed to “chronic Lyme disease” actually had fibromyalgia. Many had already received multiple courses of antibiotics before the correct diagnosis was made, and none reported their fibromyalgia symptoms resolving after antibiotic treatment.¹⁰ A false positive Lyme test, or even a real past infection that has already resolved, can anchor clinicians and patients alike on a diagnosis that delays treatment for what is actually going on.

The Old Lyme Vaccine and Test Interference

From 1998 to 2002, a Lyme vaccine called LYMErix was on the market in the United States. It targeted a protein on the surface of the Lyme bacterium called OspA. The vaccine worked, but it created a practical headache: recipients developed antibodies to OspA that caused the standard ELISA screening test to come back positive. Data from vaccinated individuals showed that the majority of vaccine recipients developed positive ELISAs, and Western blot analysis revealed that OspA vaccination induced antibodies that bound to several different Borrelia proteins, not just OspA.¹¹

LYMErix was withdrawn from the market in 2002 due to poor sales and controversy over side effects, but the diagnostic interference it caused was a recognized concern throughout its short life.¹² New Lyme vaccines currently in clinical trials have been designed to avoid this problem, but the LYMErix episode illustrates how an antibody response triggered by a vaccine, rather than a natural infection, can produce a textbook false positive. Anyone who received LYMErix in the late 1990s or early 2000s and later tested positive for Lyme may have been seeing the vaccine, not the disease.

Modified Two-Tier Testing and Where It Stands

The traditional two-tier system has been in place since the 1990s, but in recent years the CDC has endorsed an alternative called modified two-tier testing. Instead of following a positive ELISA with a Western blot, the modified approach uses a second, different immunoassay. The intended advantage is better sensitivity, particularly for early Lyme disease, and potentially faster turnaround.

In real-world data, the modified approach identified substantially more positive patients than the traditional protocol. One large study found that overall test positivity was 8.1% with the modified protocol versus 3.7% with the standard approach. Adults aged 18 and older were nearly twice as likely to test positive using the modified method, though rates were similar in children and adolescents.¹³ Separately, comparisons of modified platforms showed significantly higher sensitivity for IgG antibodies than the traditional immunoblot approach.¹⁴

The higher positivity rate raises a question that matters for false positives: is the modified protocol finding more real cases, or also picking up more false ones? The increased positivity was driven largely by IgM-positive results, which, as covered earlier, are the less specific antibody class.¹³ In endemic areas with high clinical suspicion, this likely reflects genuine gains in early detection. In low-prevalence settings, more IgM positives could mean more false alarms. The evidence is still being sorted out, and clinicians are advised to consider the clinical context just as carefully with the new protocol as with the old one.

Less Common Sources of Interference

Beyond the major categories, a scattering of other conditions have been linked to false positive results. Malaria was associated with a higher rate of falsely reactive samples in one evaluation of commercial Lyme screening tests.¹⁵ This is relevant mainly for travelers returning from malaria-endemic regions who develop febrile illness and are tested broadly for tick-borne and mosquito-borne infections.

Anti-mouse antibodies, which some people produce after exposure to certain medical treatments or diagnostic agents, can also interfere with immunoassays. A study evaluating a VlsE-based Lyme assay found that specificity dropped slightly when tested against a panel of potentially cross-reactive sera, including samples from patients with anti-mouse antibodies, prior Lyme vaccination, autoimmune conditions, and various infections, achieving about 94% specificity overall rather than the higher figure seen in uncomplicated healthy controls.¹⁶

What You Can Do About It

If you receive a positive Lyme test and you are not sure it is real, a few practical steps can help. First, confirm that the full two-tier protocol was completed. A positive screening ELISA alone is not a diagnosis. Second, consider the clinical picture: do you have symptoms consistent with Lyme, and is there a plausible exposure history involving tick bites in an endemic area? If both answers are no, the test result deserves skepticism regardless of the number on the lab report.

Tell your doctor about other conditions that could explain the result. If you have lupus, rheumatoid arthritis, a recent mono infection, or a history of syphilis, any of those could be driving the positive. If you are in a low-prevalence state and have not traveled to an endemic area, the math strongly favors a false positive over a true one. And if you were among the small number of people who received the LYMErix vaccine in the late 1990s, mention that as well.

Testing technology continues to evolve. The shift toward modified two-tier protocols and assays using recombinant antigens like VlsE and C6 peptide has improved both sensitivity and specificity compared to older whole-cell-based tests. But no serologic test is perfect, and the fundamental challenge remains: antibody-based tests detect your immune response, not the bacterium itself, so anything that stimulates a similar-looking immune response can produce a positive result that has nothing to do with Lyme disease.

1
PubMed Central. Current Guidelines, Common Clinical Pitfalls, and Future Directions for Laboratory Diagnosis of Lyme Disease, United States
2
PubMed. Cross-reactivity in serological tests for Lyme disease and other spirochetal infections
3
PubMed Central. Antibody Cross-Reactivity in Serodiagnosis of Lyme Disease
4
PubMed Central. Cross-reactivity of nonspecific treponemal antibody in serologic tests for Lyme disease
5
PubMed Central. Infectious Mononucleosis and Lyme Disease as Confounding Diagnoses: A Report of 2 Cases
6
PubMed. False positive seroreactivity to Borrelia burgdorferi in systemic lupus erythematosus: the value of immunoblot analysis
7
Oxford Academic (Clinical Infectious Diseases). Editorial Commentary: Better Laboratory Testing for Lyme Disease: No More Western Blot
8
PubMed Central. Poor Positive Predictive Value of Lyme Disease Serologic Testing in an Area of Low Disease Incidence
9
JAMA. The Overdiagnosis of Lyme Disease
10
PubMed. “Chronic Lyme disease” as the incorrect diagnosis in patients with fibromyalgia
11
PubMed Central. Effect of immunization with recombinant OspA on serologic tests for Lyme borreliosis
12
PubMed. A brief history of OspA vaccines including their impact on diagnostic testing for Lyme disease
13
PubMed Central. Real-world Lyme disease testing results using modified vs standard two-tier test protocols
14
PubMed Central. Performance of two modified two-tier algorithms for the serologic diagnosis of Lyme disease
15
Elsevier / Diagn Microbiol Infect Dis. Evaluation of commercial screening tests and blot assays for the diagnosis of Lyme borreliosis
16
Clin Vaccine Immunol / American Society for Microbiology. Evaluation of the recombinant VlsE-based liaison chemiluminescence immunoassay for detection of Borrelia burgdorferi and diagnosis of Lyme disease