Campylobacter is a major cause of bacterial foodborne diseases in both developing and developed countries, with Campylobacter jejuni contributing more than 90% of the cases reported and C. coli having a relatively minor role. There is incomplete understanding of the mechanisms by which C. jejuni/coli isolates cause human disease. A range of potential virulence determinants that include flagellum-mediated motility, invasive capability, bacterial adherence to intestinal mucosa and the ability to produce toxin have been suggested. Poultry are recognized as a major source of the organism. In this work, we have used a novel PCR-microsphere method to screen a collection of 100 C. jejuni and 38 C. coli isolates obtained from meat chickens in New South Wales for the presence of 20 putative virulence genes. The assays were performed as two 10-plex reactions. A total of 17/20 of the putative genes were detected in at least one C. jejuni isolate with 9 genes being present in more than 90% of the isolates. In contrast, just 9 genes were detected in at least 1 C. coli and all 9 were present in at least 84% of isolates. The genes found only in C. jejuni were flhA, flhB, docA, docB, cdtA, cdtB, cgtB and cadF while iamA was found only in C. coli. The PCR-microsphere approach used in this work offers considerable potential as a rapid, cost effective tool to screen isolates for putative virulence genes. This study, and subsequent studies using this approach, will provide insights into the mechanisms that are linked with the virulence of Campylobacter jejuni and Campylobacter coli.