The present knowledge about the heparin molecular structure has been reported by current scientific literature and especially the relationship between structure and function. From the pharmacological point of view the authors suggest future lines of research in this field. The role of endothelial and the mechanisms of heparin removal from the circulation (saturation and desaturation) are analyzed. From the anticoagulation point of view the authors after the analysis of the anti-thrombin III and anti-factor Xa activity, evaluate the heparin biological action on the platelets, complement, white blood cells. They also evaluate the questions collected to heparin use in non classical clinical situations, alternative routes of administration and new therapeutic and anticoagulant procedure; the association of prostacyclin together with heparin.