The second edition of the World Health Organization (WHO) classification of thymic tumors (2004) has resumed the previous separation of thymic carcinomas (TCs) from thymomas. This “reseparation” was mainly based on new genetic data. Consequently, it is no longer recommended to label TCs as type C thymomas. TCs are very heterogeneous and comprise squamous, basaloid cell, mucoepidermoid, neuroendocrine, and many other subtypes. They resemble morphologic mimics in other organs and are labeled accordingly. However, only thymic squamous cell carcinomas (TSCCs) and lymphoepithelioma-like carcinomas are relatively common. For TSCCs, quite specific immunohistochemical markers (eg, CD5, CD70, CD117, CD205, FOXN1) and chromosomal gains and losses have been defined that help to distinguish TSCCs not only from malignant thymomas but also from pulmonary squamous cell carcinomas. Recognition of these differences is clinically important, because the prognosis of TSCC is better compared with the other TC subtypes and also compared with lung tumors. Considering the need to treat advanced TC more effectively, disparate findings in predictive molecular markers (eg, KIT mutations in TSCC, but not in thymomas) suggest that targeted treatments will have to be different in thymomas and TC. Preliminary data from single case collections and small treatment trials support this prediction.