Traditional anticoagulants used in intermittent hemodialysis (HD) are unfractionated heparin (UFH) and increasingly low molecular weight heparins (LMWHs). Repeated and prolonged exposure to UFH and/or LMWHs may further disturb hemostasis in uremic patients. Vascular adhesion protein-1 (VAP-1) is secreted by vascular smooth muscle cells, adipocytes and endothelial cells with functional monoamine oxidase activity and is elevated in atherosclerosis, diabetes mellitus and obesity. The aim of this study was to assess the effects of UFH and LMWHs on VAP-1 concentration in HD patients. The effects on single HD session on VAP-1 were also evaluated as well as VAP-1 levels in regard to type of renal replacement therapy. We studied 82 hemodialyzed patients (mean age 63 years, dialysis vintage 59 months) and 17 patients treated by means of hemodiafiltration (HDF) (mean age 59 years, HD vintage 84 months, HDF 7 months). Patients were anticoagulated with enoxaparin (n = 46), dalteparin (n = 10), nadroparin (n = 6) or UFH (n = 20) during their HD sessions. VAP-1 was assessed using kits from BioVendor, Modrice, Czech Republic. Patients on HDF had significantly lower VAP-1 when compared with HD patients. We found that VAP-1 concentration in patients dialyzed by using LMWH or UFH was similar. There was no effect on HD session on VAP-1 concentration. Diabetic patients had higher serum VAP-1 than non-diabetic. HDF is associated with lower VAP-1 levels indicating less pronounced endothelial cell injury than hemodialysis. Type of heparin seems to have no effect on VAP-1 levels in hemodialyzed patients. However, the cross-sectional but not prospective design is a limitation of this study.