The Philadelphia negative chronic myeloproliferative neoplasms are hematological disorders with several diagnostic challenges. Due to recent molecular findings, the WHO classification of Tumors of Hematopoietic and Lymphoid Tissue 2008 reorganized the field of chronic myeloproliferative diseases. Thus, specific molecular markers provide important information for current diagnostic strategies. This review highlights the important diagnostic tools in classical and atypical myeloproliferative neoplasms mainly the JAK2V617F mutation, the Mpl receptor, Polycythemia rubra vera 1 (PRV1), platelet-derived growth-factor receptor alpha (PDGFRA), platelet-derived growth-factor receptor beta (PDGFRB), fibroblast growth-factor receptor 1 (FGFR1) and c-kit tyrosine kinase. A description of the origin, clinical correlations and role in diagnosis and therapy is provided for each of these molecular markers.