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Summary Patient-derived organoids maintain functional and phenotypic characteristics of the original tissue such as cell-type diversity. Here, we provide protocols on how to label intestinal (cancer) stem cells by integrating the stem cell ASCL2 reporter (STAR) into human and mouse genomes via two different strategies: (1) lentiviral transduction or (2) transposon-based integration. Organoid technology, in combination with the user-friendly nature of STAR, will facilitate basic research in human and mouse adult stem cell biology. For complete details on the use and execution of this protocol, please refer to Oost et al. (2018)., Graphical Abstract, Highlights • Choose the optimal STAR plasmid suited for your research • Tips and tricks on how to prepare organoids for STAR integration • Diverse protocols for STAR integration: lentiviral and transposon-based approaches, Patient-derived organoids maintain functional and phenotypic characteristics of the original tissue such as cell-type diversity. Here, we provide protocols on how to label intestinal (cancer) stem cells by integrating the stem cell ASCL2 reporter (STAR) into the human and mouse genome via two different strategies: (1) lentiviral transduction or (2) a transposon-based system. Organoid technology, in combination with the user-friendly nature of STAR, will facilitate basic research in human and mouse adult stem cell biology.