The aim of our studies was to evaluate rep-PCR typing using different primers as a fast genotyping method for discrimination of C. jejuni. Also a microfluidic electrophoretic DNA separation method for rapid DNA fingerprinting based on Lab-on-a-Chip technology was tested. Based on the test results, the single polytrinucleotide (GTG)₅ was chosen as primer. Nine strains representing three epidemiological groups from the CAMPYNET network strains were assigned to three different groups by both (GTG)₅- PCR and PFGE. Typing of 72 epidemiologically independent strains using (GTG)₅-PCR and PFGE clustered the strains in 60 and 53 clusters, respectively, with an identical discriminatory power (D=0,99). When PCR-products were separated on the Agilent 2100 Bioanalyzer Lab-on-a-Chip device the strains were grouped with the same discriminatory power, though some strains were clustered differently compare to gel-based DNA amplicon separation. The main disadvantage of (GTG)₅-PCR typing was differences in band intensity that complicates comparison of (GTG)5-PCR fingerprints when numerous strains are evaluated. The advantages of rep-PCR based subtyping were rapidity, simplicity, similar discriminatory power to PFGE and possible rapid DNA amplicon separation based on Lab-on-a-Chip technology with Agilent 2100 Bioanalyzer.