Broiler chickens are created through genetic selection and are fast-growing, highly efficient chickens for human meat consumption. In the past, antibiotics have been used preventively to achieve high production performances. Antibiotic resistance, however, has become one of the biggest threats for global health, and therefore Europe banned in-feed antibiotic growth promoters from livestock feed in 2006. After the ban, intestinal health problems in broilers significantly increased. Those intestinal health problems are often associated with an imbalance in the microbiota. Microbiota is defined as the assemblage of living microorganisms present in a defined environment. Knowledge on the development and variation of the intestinal microbiota will be of great value to optimize the health of broilers and to prevent the need for therapeutic antibiotics. The objective described in this thesis is to improve the understanding of the interaction between the intestinal microbiota and broiler health. The first part of the thesis is about how to design intestinal microbiota research in poultry. The second part of this thesis focuses on if phenotypic characteristics can explain the intestinal microbiota composition and its variation in poultry farms. In the third part, the focus shifts from observational studies to intervention studies.