In most European countries human campylobacteriosis is the most important bacterial zoonotic foodborne infection. Chicken meat is considered the main source of infection. Since most strategies assessed so far, in reducing Campylobacter colonization in chickens or in the reduction of human disease, have not been very effective, new knowledge regarding Campylobacter"s interaction with the host is needed. In this study we analysed fecal and cecal samples of five chicken flocks of different Austrian farms for the occurrence of Cjejuni and C. coli, and analysed the intestinal microbiota by PCR-SSCP, cultural detection of lactic acid bacteria, Enterococci, Staphylococci, Enterobacteriaceae, E. coli, and total aerobic colony counts. Furthermore ten chicken samples of cecal content of a flock during colonization with Campylobacter spp. was analysed by high throughput sequencing. With all three methods used we could detect a change within the microbiota caused by Cjejuni. Enumeration of different bacteria was significantly lower in fecal samples positive for C. jejuni, pointing out that a higher water content and thus, a preliminary stage of diarrhea might appear during Campylobacter colonization. By PCR-SSCP analysis the microbiota composition differed between colonized and non-colonized chicken fecal samples. This could also be detected in community analysis by high throughput sequencing, but this difference was only a tendency and not statistically significant. It can be concluded that C. jejuni is interacting with the intestinal microflora in their respective hosts and hence, this has to be taken into account when providing new strategies to combat Campylobacter colonization and disease.