Ph(-) myeloproliferative neoplasms (MPN) are divided into three different entities including Essential thrombocythemia (ET), Polycythemia vera (PV) and Primary myelofibrosis (PMF). Thrombosis as the most common complication occurs in about 20-40% of patients. Aim of this study was to investigate genetic and hematologic prothrombotic risk factors in Ph(-) MPN patients. For this purpose we analyzed anamnestic status and blood samples of 258 Ph(-) MPN adult patients (134 ET, 70 PV and 54 PMF) and 258 healthy controls (without thrombosis) matched by age and sex. Different types od polymerase chain reactions (PCR) were performed for detection of FV Leiden, FII G20210A, human platelet antigens (HPA-1, -2, -3, -5), P-selectin (P-SEL S290N, N562D, V599L, T715P) and P-selectin glycoprotein 1 ligand (PSGL-1 M62I) polymorphisms. Blood counts were performed at diagnosis as well as detection of V617F mutation in JAK2 gene by allele specific PCR, and for V617F positive patients mutation burden allele was determined by real time quantitative PCR. Seventy-nine patients experienced 109 thrombotic events in total, 59 patients (29 ET, 19 PV and 11 PMF) had arterial thrombosis and 26 patients (10 ET, 8 PV and 8 PMF) venous thrombosis. In the group of ET patients leukocytosis, hyperlipidemia and V617F mutation increased risk for thrombosis, while for carriers of HPA-5b allele this risk was decreased. In PV patients those with diabetes had higher risk for thrombosis while in carriers of HPA-2b risk was much lower. PMF patiens with allele 290N had higher risk for thrombosis. This study brought some new findings of the thrombosis etiology in Ph(-) MPN patients.