The cancer stem cells (CSCs) are biologically distinct subset of rare cancer cells with inherent ability of self-renewal, de-differentiation, and capacity to initiate and maintain malignant tumor growth. Studies have further reported that CSCs prime cancer recurrence and therapy resistance. Therefore, targeting CSCs to inhibit cancer progression has become an attractive anti-cancer therapeutical strategy. Recent technical advances have provided a greater appreciation of the multistep nature of the oncogenesis and also clarified that CSC concept is not universally applicable. Irrespective, the role of the CSCs in gastrointestinal (GI) cancers, responsible for the most cancer-associated death, has been widely accepted and appreciated. However, despite the tremendous progress made in the last decade in developing markers to identify CSCs, and assays to assess tumorigenic function of CSCs, it remains an area of active investigation. In current article, we review findings related to the role and identification of CSCs in GI-cancers and discuss the crucial pathways involved in regulating CSCs populationsâ development and drug resistance, and use of the tumoroid culture to test novel CSCs-targeted cancer therapies.