Thymic malignancies are extremely rare although usually affect young adults and continue to remain an important health problem. Like other rare diseases, progress in thymic malignancies has been slow and the treatment cornerstone still remains surgical resection. Next generation sequencing and other advances in molecular biology are shedding light onto the multiple genetic aberrations involved and have opened a new field for research with molecularly targeted therapies such as CKIT inhibitors or anti-EGFR therapies. In this review we will summarize the current knowledge in the pathophysiology, diagnosis, prognosis and latest advances in the management of thymomas and thymic carcinomas.