Thymoma is the most common anterior mediastinal tumor in adults and is frequently associated with autoimmune disorders such as myasthenia gravis. Thymomas are a diverse group of epithelial neoplasms with a behavioral spectrum that spans the complete clinical gamut from entirely benign to highly aggressive, lethal thymic carcinomas. The biologic behavior seems to depend primarily on the clinical stage at presentation and histologic subtype. This article discusses thymic organogenesis, Masaoka staging, WHO histologic classification of thymoma and thymic carcinoma, and selected molecular characteristics that highlight this diversity. This discussion will further underscore both the similarities and differences between categories of thymic epithelial neoplasms and offer support for the notion that tumor heterogeneity and/or tumor progression may explain the observed clinical variation in behavior. Recommendations are offered for future investigational approaches to further the understanding of the complexity of these tumors.