Thymoma is one of the most common solid tumors in the mediastinum. The histological classification of thymic epithelial tumor includes non-invasive thymoma, invasive thymoma and rare thymic carcinomas. Although several clinico-pathological and immunological studies of thymoma have been reported, little is known of the genetic alterations that occur in the tumorigenesis of thymoma. In this review, we would mention about several gene expression abnormalities in thymoma, including (1) p53, which is mutationally inactivated in many tumors; (2) matrixmetalloproteinases (MMPs), that may play important roles in tumor invasion and metastasis; (3) Epidermal growth factor receptor (EGFR), which is important in normal and neoplastic epithelial cell growth and is an attractive therapeutic target, as reviewed recently; and (4) genes at chromosome 6, which suffers frequent and multiple aberrations in thymoma. Finally, using oligonucleotide arrays to monitor in vivo gene expression levels in the early and late stage thymoma tissues, two candidate genes were identified that were more highly expressed in the advanced stage thymomas. One was a wellknown gene, c-JUN and another was an unknown gene, AL050002.