Thymomas and thymic carcinomas (TC) are rare epithelial tumors of the thymus. Although most thymomas have organotypic features (i.e., resemble the normal thymus), TC are morphologically undistinguishable from carcinomas in other organs. Apart from their different morphology, TC and thymomas differ also in functional terms (TC, in contrast to thymomas, have lost the capacity to promote the maturation of intratumorous lymphocytes), have different genetic features (discussed in this review), a different immunoprofile (most TC overexpress c-KIT, whereas thymomas are consistently negative), and different clinical features (TC, in contrast to thymomas, are not associated with paraneoplastic myasthenia gravis). Thus, although all the data suggest that the biology of thymomas and TC is different, in clinical practice, their therapeutic management up to now is identical. In the age of personalized medicine, the time may have come to think this over. We will briefly review the molecular genetics of malignant thymic tumors, summarize the current status of targeted therapies with an emphasis on the multitargeted kinase inhibitors sunitinib and sorafenib, and try to outline some future directions.