Rare tumors pose significant challenges to clinical research, diagnosis, and therapy due to their low incidence, high molecular heterogeneity, and the lack of preclinical models.Conventional patient-derived cell lines and patient-derived tumor xenografts have significant limitations in recapitulating the characteristics of rare tumors. As an emerging in vitro biological model, organoids preserve the molecular characteristics of original tumors and possess high biological relevance, efficient amplification capabilities, and potential for personalized medicine applications. They have currently been applied in the research of various rare tumors. This review summarizes current research on organoid models of rare tumors derived from different tissue origins, and outlines current challenges and future development directions.