Determination of the genetic markers by the application of new genomic methodologies has provided important insight into the pathogenesis of mediastinal disease. These new techniques have enabled scientists to uncover differential gene expression patterns between subtypes of thymomas, correlate tumor marker expression with germ cell tumors, and determine a link between the NF-kappaB and JAK/STAT pathways with Hodgkin's and non-Hodgkin's lymphoma. Despite the progress made in the understanding of genetic markers of select mediastinal tumors, significantly more investigation is required to elucidate the molecular pathways involved in the pathogenesis of these tumors.