A novel panel of peptide for serological identification of Borrelia burgdoferi sensu stricto, Borrelia garinii and Borrelia afzelii was developed and assessed in this study. The diagnostic algorithm of the novel test was initially trained testing 10 US human sera including 3 early-stage and 3 late-stage Lyme disease positive sera, 2 sera positive for Babesia and 2 sera positive for Syphilis, all purchased from a private biorepository. Findings were then corroborated testing (a) 33 additional EU follow-up positive sera from seroconverted patients bitten by ticks that tested positive for B. burgdorferi sensu stricto (No 2), Borrelia garinii (No 14), Borrelia afzelii (No 15) Borrelia valaisiana (No 2), and (b) 40 negative sera from US healthy donors. Results of preliminary US sera testing showed successful detection of IgM and IgG antibodies and correct identification of Borrelia burgdorferi sensu stricto in all the samples tested. Analysis of EU follow-up sera showed much higher sensitivity and accuracy when IgM and IgG were tested combined together rather than separately. Sensitivity and accuracy in species identification of the anti-IgM + IgG multiplex peptide ELISA was 93.5 % and 96.5 % respectively; lower test performance was observed when IgM (i.e. sensitivity = 58.1 %; correct identification = 88.8 %) and IgG testing (i.e. sensitivity = 74.1 %; correct identification = 96.5 %) were carried out separately. Overall specificity of the anti-IgM, anti-IgG and anti-IgM + IgG multiplex peptide ELISA calculated on a total number of 46 negative sera included in this study was 91.3 %, 95.6 and 93.4 %, respectively.