Development of the gut microbiota in chickens occurs immediately after hatching and is influenced by both genetic and external factors like diet and environment (Apajalahti et al., 2004). It was reported that disturbances in the intestinal microbiota leads to a delay in growth, weakens the host resistance and increases the susceptibility to various infectious diseases (Lan et al., 2004). Gong et al. (2002) demonstrated that the cecal microbiota protects chickens against bacterial infections, while microbiota in the small intestine contributes significantly to its function, including digestion and nutrient absorption, which significantly determines the growth rate of the bird. Studies on gut microbiota have mostly been performed with chickens older than 1 week of age due to the various influences in day-old birds. However, the composition of gut microbiota at the first day of life in newly hatched chickens is a matter of interest within a longitudinal study. Therefore, the focus of the actual study was to determine the diversity and community structures of the microbiota within the small and large intestine from hatch until 4 weeks of age. Furthermore, differences among the mucosa-associated and luminal content microbiota were determined for the first time.