Adult stem cells are crucial for maintaining proper function and repair of tissues. The epithelium of the adult mammalian intestine is a constant dialog with its underlying mesenchyme to direct progenitor proliferation, lineage commitment, terminal differentiation and ultimately cell death. The epithelium is shaped into spatially distinct compartments that are dedicated to each of these events. The unique intestinal orchestration makes the crypt as one of the most accessible models for the study of adult stem cell biology (Barker et al., 2007). Because intestine is one of the most rapidly regenerated tissues in the body, the intestinal crypt has provided an informative system for studying stem cell biology. The full potential of these models was not realized, however, duo to the limited availability of optimized protocols and unique stem cell markers to identify the location and numbers of ICSs as well functional assays to validate the models in vivo. Though Intestinal stem cell represented by crypt population has been established in mice and human but the understanding of the underlying mechanism was not reported in other animal species in detail. The present research focussed on the isolation of intestinal crypts and their in vitro culture characteristics in chicken, a mammalian animal model widely used for research and food application has been carried out using cytochemical and fluorescent activated cell sorting for stem cell specific marker Sox 9.