We report a case of atypical polypoid adenomyoma (APA) concomitantly identified with complex atypical endometrial hyperplasia (CAH) in the uterus. Since an initial endometrial smear revealed atypical endometrial cells, a diagnosis of CAH was made. Even though a concomitantly performed uterine cervical smear contained both atypical epithelial and stromal cells, the diagnosis of APA was not initially made because the cytological criteria for APA had not been established. Histologically, we recognized both CAH in the uterine corpus and APA in the lower uterine segment in the hysterectomy material. Retrospectively, the cells in the first cervical smear were interpreted as part of APA because the same types of cells were observed in the intraoperative cytology sample. Although the APA and CAH lesions were interposed by normal endometrium, estrogen was suspected to be the common etiological factor. Reports regarding the cytology of APA are currently scarce. To our knowledge, this is the first report showing cytological presentation of association of APA with CAH in addition to the first cervical smear of APA containing both epithelial and stromal components. Identification of abnormal proliferation of epithelium and stromal cells of smooth muscle origin is useful in the cytological diagnosis of APA.