Thymomas are malignant, epithelial tumors of the thymus of diverse morphology that may metastasize or relapse after resection. The WHO histological classification includes five main subtypes A, AB, B1, B2 and B3. Types A and AB usually harbour a specific GTF2I gene mutation. Thymolipomas are very rare, benign tumors composed of thymic parenchyma and adipose tissue. We present the case of a 37-year-old male with an incidentally found mediastinal tumor that shared morphological features of a thymoma of unknown histological type and a thymolipoma-like tumor. Microscopically the tumor contained three components: (I) a highly organoid component that reproduced the thymic parenchyma with numerous Hassall corpuscles; (II) a lymphocyte-poor, epithelial component; (III) mature adipose tissue. A wide panel of immunohistochemical tests was used, but the results were not decisive for differential diagnosis. Genetic analysis of GTF2I, BRAF and NRAS genes revealed no mutations. The tumor was completely resected. The patient did not receive adjuvant radiotherapy. A 1.5 years after resection there was no evidence of tumor recurrence. Based on our case we carefully analyse and compare the microscopic features of thymoma vs. thymolipoma. The differentiation between these tumors is crucial due to their distinct clinical course and required therapeutic approach.