A multiplex-bead-based assay for the detection of serum antibodies to Borrelia burgdorferi sensu lato was evaluated. The assay contained 13 different antigens in both the IgG and the IgM assay; thus, a total of 26 measurement results were available from each sample. A total of 49 Danish patients with Lyme neuroborreliosis (LNB), 218 Danish blood donor controls, a set of 61 Swedish patients with LNB and 139 Swedish non-LNB patients investigated for suspected LNB were used. There are four parts developed in this study: a characterization of the sero-epidemiological antibody-response pattern, the construction of a diagnostic score, evaluation of the scoring method using an independent dataset and an assessment of the analytical quality of the multiplex assay. The VlsE IgG had the highest diagnostic value with an AUC (area under the curve) of 96% on the receiver operating characteristic curve. The OspC IgM had AUCs just above 80%. All the other antigens had both low quantitative reactivity and lower contrast in the patients with LNB compared to controls. The diagnostic value of the assay may be improved by using a logistic model giving a sensitivity of 90 and 79% for the specificities at 92 and 98%, respectively. Overall, the patients with LNB had serum reactivity in IgG VlsE, but modest antibody reactivity in the remaining 12 IgG and 13 IgM antibody measurements. Using a logistic regression model with five IgG and two IgM antigens, the sensitivity and specificity of the assay was improved; but the IgG VlsE component alone contributed most of the diagnostic contrast.