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Adenomatoid tumor is a rare benign neoplasm of mesothelial origin occurring in various anatomical locations, including the uterus. In this article, we describe an adenomatoid tumor of the uterus exhibiting severe nuclear atypia in the clinical context of long-term hormone therapy. The patient was a 51-year-old woman who underwent total abdominal hysterectomy with bilateral salpingo-oophorectomy for uterine leiomyomas. Gross evaluation of the uterus revealed multiple intramural and subserosal unencapsulated nodules that were both well and poorly circumscribed and measured from 4 to 25 mm. Microscopically, one of the nodules consisted of hyperplastic leiomyocytes intermixed with irregular vascular-like and tubular spaces lined by flattened cells that occasionally showed moderate to severe nuclear atypia (enlargement, hyperchromasia, and multinucleation). Bizarre pleomorphic cells were also present. Mitotic activity was minimal. The tumor cells showed diffuse positivity for calretinin, keratin AE1/AE3, L1 cell adhesion molecule, and podoplanin, while CD31, CD34, epithelial membrane antigen, HMB45, MDM2, and S100 protein stains were negative. Expression of BRCA1-associated deubiquitinase 1 and methylthioadenosine phosphorylase was retained. This immunophenotype supported a mesothelial origin of the neoplastic cells, leading to the final diagnosis of adenomatoid tumor with marked nuclear atypia. Unusual histopathological findings in adenomatoid tumors, such as marked nuclear atypia and pleomorphism, may pose significant diagnostic challenges and result in misdiagnosis. Despite these unusual features, the tumor in our study showed no evidence of aggressive behavior or malignant transformation. Although we hypothesize that these changes may be related to prolonged hormone therapy, their pathogenesis and clinical significance remain unclear, underscoring the need for further investigation.