Axenic (germ-free) rodents have become increasingly used to study the role and functioning of the gut micobiota and its association with diseases. These models are also a critical resource in our advancement in the understanding of the host-microbiome relationships. However, the generation and maintenance of these specialized rodents is labor-intensive and requires vigilance while conducting their routine daily animal husbandry to minimize any potential contamination threats. In this presentation, we will review methods to generate germ-free rodents using different techniques (embryo transfer/cesarean rederivation). Recommendations for a variety of different housing options along with preventative methods to avoid microbiological contamination during their daily husbandry will be provided. Finally, recommendations for sampling collection, testing methods and frequencies will be discussed to ensure the germ-free status of the animals.