Outdoor access is an important part of organic and free-range poultry production, yet limited information exist on the effect of various housing and production systems on the growth performance and colonization of food-borne pathogens. Therefore, the primary purpose of the current study was to evaluate the influence of different housing systems (particularly fixed versus small, portable houses, with and without outdoor access to pasture) and different broiler genotypes on the gastrointestinal bacteria in broilers. The fundamental factor studied was the presence of any quantitative changes in common gastrointestinal microbiota, including pathogenic genera such as Campylobacter sp. and Salmonella sp. The results showed differences in intestinal microbiota and confirmed lowered counts of caecal coliforms in pasture-reared broilers.