Various carcinogenesis steps, including tumor development, progression, metastasis, and recurrence, contribute to cancer heterogeneity. Heterogeneity may lead to drug resistance in cancer treatment; therefore, it is crucial to establish cancer models that can retain the biological properties of human tumors, including heterogeneity, for elucidating the mechanisms underlying cancer pathogenesis, validating candidate drugs, and implementing precision medicine. Owing to its ability to retain the histological and molecular characteristics of the original tumor and its high success rate in primary cancer cell culture, organoid culture has garnered considerable attention. Consequently, patient-derived organoids have been generated from the clinical samples of various cancer types. Since we have pioneered the organoid-based research field, particularly in gynecologic cancers, herein, we provide an overview of the organoid culture and its applications in cancer research, focusing on the current status of organoid-based research on endometrial and cervical cancers. Additionally, the challenges and perspectives associated with organoid culture techniques in basic and translational cancer research have been discussed.