An identification scheme based on restriction fragment length polymorphism of polymerase chain reaction products (PCR-RFLP) was developed to differentiate isolates of the genera Campylobacter, Arcobacter and Helicobacter. Based on the 16S rRNA gene of these genera, PCR amplified a 1216-bp fragment. The amplicons were digested with the restriction enzymes RsaI and EcoRV. Additional differentiation was obtained using a PCR-assay based on the hippuricase gene. Genotyping was performed on several reference strains from the National Collection of Typing Culture (NCTC), London, and on 130 field isolates. In parallel, a phenotypic differentiation was performed, in order to compare the results. In 119 cases (91.5%) the results obtained from the genotypic characterization were concordant with those from phenotypic testing. Co-infections with Campylobacter jejuni and Campylobacter coli in two samples and seven hippurate-negative C. jejuni-strains were identified by the genotypic method. Furthermore, PCR-RFLP assays identified an atypical isolate as Campylobacter fetus/hyointestinalis.