The diagnosis of synchronous carcinomas is difficult in all types of cancer. However, in gynecological cancers, synchronous endometrial and ovarian carcinomas are rarely seen and are more difficult to diagnose because the uterus and ovaries are adjacent organs. Although classical pathological criteria have been used for diagnosis, molecular biological methods are increasingly being used to refine diagnostic decisions. Through genomic analyses, such as next-generation sequencing and targeted and exome sequencing, many cases that have been diagnosed and treated as primary synchronous carcinomas have been determined to actually be metastatic carcinomas. It is necessary to establish new diagnostic criteria by incorporating molecular biological methods with conventional pathological diagnosis.