The NHS relies on two-tier antibody testing. When the body has an infection it usually produces antibodies against the bacteria. For Lyme this is also true in the early stage and the NHS system may be adequate. The ELISA test is run first and a confirmatory, more specific and more sensitive, Western Blot is then run to detect antibodies against the bacteria.  In cases of a known tick bite and rash treatment should be started without waiting for positive test results as it takes several weeks before the positive antibodies may be produced.

There are a number of problems with these tests and this testing strategy in later stages of Lyme. The NHS Western Blot ignores several key antibodies as these were used for a vaccine so would be present in healthy vaccinated people, however this vaccine was only ever used in the US. Lyme causes an undulatory antibody response so a positive one week might be a negative the next week. Some people may not produce antibodies against the Lyme bacteria at all due to their genetic make-up, due to early but insufficient antibiotic treatment or due to immune suppressing drugs such as steroids being administered. The longer the infection has been present, the less likely that there is bacteria in the blood stream for the immune system to detect too. Finally, there is some evidence that Lyme can cause immune suppression which could also potentially cause a false negative test result.

Whilst optimally a diagnosis should be clinical, additional tests can be run to help support a diagnosis of Lyme. This can include a Western Blot with all the antibodies looked for, an Elispot-LTT which looks at levels of immune cytokines released when T-cells come into contact with the bacteria, immunofluorescence or PCR to look for the actual bacteria or a test to look for immune suppression by a reduced subset of natural killer cells (CD57). The gold standard is to culture the bacteria from a patient's blood but this test has not been optimised and validated yet.