Lyme diagnosis and testing can be very confusing, which has contributed to false positive diagnoses and unnecessary treatment.
According to the CDC:
- Patients who have had Lyme disease for longer than 4-6 weeks, especially those with later stages of illness involving the brain or the joints, will almost always test positive.
- A patient who has been ill for months or years and has a negative test almost certainly does not have Lyme disease as the cause of their symptoms.
- Serologic testing is generally not useful or recommended for patients with single EM rashes. For this manifestation, a clinical diagnosis (alone) is recommended.
A 2016 systematic review  that included 8 studies of test performance in “Late Lyme” showed Lyme antibody testing to be 99.4% sensitive and 99.3% specific**.
In other words, out of 100 people with Late Lyme disease, 99-100 of them will test positive. Out of 100 people who may believe they have Late Lyme disease but do not, 99-100 of them will test negative.
Avoid unnecessary and unscientific testing
Don’t test for Lyme disease as a cause of musculoskeletal symptoms without an exposure history and appropriate exam findings. 
The CDC has expressed similar sentiments  to the ACR and has also warned against unvalidated testing [5, 9]. Quackwatch  and Science-Based Medicine  both provide accessible explanations about the differences between validated and unvalidated tests.
The CDC “describes the steps required to properly test for Lyme disease” as follows:
The first required test is the Enzyme Immunoassay (EIA aka ELISA) or Immunofluorescence Assay (IFA). If this test yields negative results, the provider should consider an alternative diagnosis. Or in cases where the patient has had symptoms for less than or equal to 30 days, the provider may treat the patient and follow up with a convalescent serum.
If the first test yields positive or equivocal results, two options are available:
1) if the patient has had symptoms for less than or equal to 30 days, an IgM Western Blot is performed;
2) if the patient has had symptoms for more than 30 days, the IgG Western Blot is performed.
The IgM should not be used if the patient has been ill for more than 30 days.
LymeScience recommends against:
- Tests from any of the following labs: IgeneX, DNA Connexions, Galaxy Diagnostics, Medical Diagnostic Laboratories (MDL), Milford Molecular Diagnostics Laboratory, Advanced Lab, Fry Laboratories, Ceres Nanosciences (Nanotrap), Global Lyme Diagnostics, Pharmasan Labs (iSpot Lyme), Coppe Laboratories (myLymeTest), ArminLabs, BCA-Lab (formerly known as Infectolab), Australian Biologics, Melisa Labs, R.E.D. Labs
- Any lab on Quackwatch’s list of “Laboratories Doing Nonstandard Laboratory Tests“.
- CD57 testing
- Diagnosis with microscopy, e.g. Live Blood Cell Analysis.
- Diagnosis based on magical beliefs, for example applied kinesiology a.k.a Autonomic Response Testing (ART)
- Urine tests
- Electrodermal testing
- Failing to follow testing strategies recommended by the CDC or local infectious diseases organizations
- Clinical diagnosis without a science-based rationale
- Diagnosis from an unscientific practitioner, including those who market themselves using the following terminology: Lyme literate (especially those affiliated with ILADS), integrative, functional, alternative, complementary, Traditional Chinese Medicine, holistic, natural, Biological, Ayurvedic, chiropractic, naprapathic, homeopathic, and naturopathic.
- Any testing not recommended by the CDC.
See also the following LymeScience pages:
- How chronic Lyme recruits followers
- Lyme misdiagnosis illustrated
- Red flags of chronic Lyme quackery
- CDC scientist: Why bands 31 and 34 aren’t used to test for Lyme disease
Other misconceptions about Lyme disease diagnosis and testing are discussed below.
Like tests for other infections like HIV, testing for Lyme disease involves looking for antibodies produced by the immune system in response to infection. This is called serologic testing because the antibodies are found in blood serum.
Testing positive for antibodies is called seropositive and testing negative for antibodies is called seronegative.
Table excerpted and reformatted* from the longer 2013 paper (ref 2 below, which is worth reading):
There is substantial evidence supporting the accuracy of FDA-cleared tests once antibodies build up in the body (4-6 weeks post-infection).
The CDC concurs:
You may have heard that the blood test for Lyme disease is correctly positive only 65% of the time or less. This is misleading information. As with serologic tests for other infectious diseases, the accuracy of the test depends upon the stage of disease. During the first few weeks of infection, such as when a patient has an erythema migrans rash, the test is expected to be negative.
Several weeks after infection, currently available ELISA, EIA and IFA tests and two-tier testing have very good sensitivity.
It is possible for someone who was infected with Lyme disease to test negative because:
- Some people who receive antibiotics (e.g., doxycycline) early in disease (within the first few weeks after tick bite) may not develop antibodies or may only develop them at levels too low to be detected by the test.
- Antibodies against Lyme disease bacteria usually take a few weeks to develop, so tests performed before this time may be negative even if the person is infected. In this case, if the person is retested a few weeks later, they should have a positive test if they have Lyme disease. It is not until 4 to 6 weeks have passed that the test is likely to be positive. This does not mean that the test is bad, only that it needs to be used correctly. 
* LymeScience reformatted the table and added punctuation, emphasis, a note, and changed the word “evidence” to “science”. Excerpted for educational and commentary purposes.
** 99.4% sensitive (95% confidence interval: 95.7–99.9) and 99.3% (95% confidence interval: 98.5-99.7%) specific.
1. Choosing Wisely: American College of Rheumatology
2. Halperin JJ, Baker P, Wormser GP. Common misconceptions about Lyme disease. Am J Med. 2013 Mar;126(3):264.e1-7.
3. CDC: Three Sudden Cardiac Deaths Associated with Lyme Carditis — United States, November 2012–July 2013
4. CDC: Lyme disease: Diagnosis and Testing
5. CDC: Lyme disease: Laboratory tests that are not recommended
6. CDC scientist Barbara J.B. Johnson, PhD: Book chapter of “Lyme disease: An Evidence-Based Approach”: Laboratory Diagnostic Testing for Borrelia burgdorferi Infection
7. CDC: “I have heard that the diagnostic tests that CDC recommends are not very accurate. Can I be treated based on my symptoms or do I need to use a different test?” Lyme FAQ.
8. Waddell LA, et al. The Accuracy of Diagnostic Tests for Lyme Disease in Humans, A Systematic Review and Meta-Analysis of North American Research. PLoS ONE. 2016;11(12):e0168613.
9. CDC: Notice to Readers: Caution Regarding Testing for Lyme Disease
10. Quackwatch: Some Notes on Nonstandard Lyme Disease Tests
11. Science-Based Medicine: Lemons and Lyme: Bogus tests and dangerous treatments of the Lyme-literati
12. American Lyme Disease Foundation: Limitations of Antibody-Based Diagnostic Tests for Lyme Disease
13. Botman E, et al. Diagnostic behaviour of general practitioners when suspecting Lyme disease: a database study from 2010-2015. BMC Fam Pract. 2018;19(1):43.
14. Article about “ELISpot” Lyme tests: New test has no added value in Lyme disease of the central nervous system
15. Duerden BI. Unorthodox and unvalidated laboratory tests in the diagnosis of Lyme borreliosis and in relation to medically unexplained symptoms. Department of Health, London, UK, 2006.
16. CDC Q and A: Epidemiology and Clinical Features of Lyme Disease
17. Choosing Wisely: Lyme Disease
18. Canadian scientists: Lyme disease: How reliable are serologic results?