The diagnosis of Lyme disease is difficult because tests that reflect activ
e disease or have reasonable sensitivity and specificity are lacking or not
timely. Molecular methods are controversial because of differences in assa
ys, gene targets, and limited clinical validation. This review summarizes p
ublished assays for Lyme disease diagnosis using skin, plasma, synovial flu
id, cerebrospinal fluid (CSF), and urine. Meta-analyses show the strengths
and weaknesses of these methods. Overall, assays for skill and synovial flu
id (68% and 73%, respectively) have high sensitivity and uniformity. The lo
w rest sensitivity of CSF (18%) and plasma (29%), variable sensitivities am
ong CSF and urine assays, and persistence of Borrelia burgdorferi DNA in ur
ine and synovial fluid even with therapy and convalescence make these unsui
table for primary diagnosis. Molecular assays for Lyme disease are best use
d with other diagnostic methods and only in situations in which the clinica
l probability of Lyme disease is high.