Spirochaetes of the Borrelia burgdorferi sensu lato complex, which includes those that cause Lyme disease, have not been identified in Australia. Nevertheless, Australian patients exist, some of whom have not left the country, who have symptoms consistent with so-called "chronic Lyme disease". Blood specimens from these individuals may be tested in Australian laboratories and in specialist laboratories outside Australia and sometimes conflicting results are obtained. Such discrepancies cause the patients to question the results from the Australian laboratories and seek assistance from the Australian Government in clarifying why the discrepancies occur. The aim of this study was to determine the level of agreement in results between commonly used B. burgdorferi serology assays in specimens of known status, and between results reported by different laboratories when they use the same serology assay. Five immunoassays and five immunoblots used in Australia and elsewhere were examined for the detection of IgG antibodies to Borrelia burgdorferi sensu lato. Predominantly, archived specimens previously tested for Lyme disease were used for the study and included 639 contributed by seven clinical laboratories located either in Australia or in areas endemic for Lyme disease. Also included were 308 prospectively collected Australian blood donor specimens. All clinical specimens were tested in all 10 assays whereas blood donor specimens were tested in all immunoassays and a subset was tested on immunoblots. With the exception of one immunoblot, the results between the assays agreed with each other in a known positive specimen population ≥ 77% of the time and in a known negative population, 88% of the time or greater. The test results obtained during the study were different from the participating laboratory's less than 2% of the time when the same assay was used. These findings suggest that discordance in results between laboratories is more likely due to variation in algorithms or in the use of assays with different sensitivities or specificities rather than conflicting results being reported from the same assay in different laboratories. In the known negative population, specificities of the immunoassays ranged between 87.7% and 99.7%. In Australia's low prevalence population, this would translate to a positive predictive value of < 4%.