The first possibly causative molecular aberration in patients with myeloproliferative disorders has recently been described. A point mutation in the Janus kinase 2 exchanging a valine for a phenylalanine at position 617 (JAK2 V617F) was found in 65% to 97% of polycythemia vera (PV) patients, as well as in approximately 50% of essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF) patients. In addition, a growing set of molecular and genetic markers, some possibly contributing to disease development, some more likely epiphenomena, has been characterized in these patients over the last few years. Compiling and synthesizing the increasing knowledge on the genetic changes observed in myeloproliferative disorder (MPD) patients will allow us to generate testable hypotheses on the molecular etiology of disease development. Therefore, this review will summarize the current knowledge on chromosomal aberrations, molecular markers, and gene expression studies in MPD patients. From these data, a model depicting our current understanding of the interplay between these markers is presented.