Antithrombin (AT) and heparin cofactor II (HCII) are members of serpin super family and the physiological inhibitors of thrombin in the circulation. They are under control of glycosaminoglycans (GAGs) from the vessel wall, which play a key role in accelerating and localizing their action. Thrombin inhibition by AT requires a specific AT-binding pentasaccharide sequence in heparan sulfate (HS)/heparin and a longer GAG chain to allow the bridging of AT and thrombin exosite II.  In contrast, HS/heparin does not possess a high affinity sequence for HCII. Furthermore, dermatan sulfate (DS) activates HCII, but has no effect on AT. Thrombin inhibition by HCII seems involve allosteric GAG-induced interaction of an acidic N-terminal domain of HCII with thrombin exosite I. This proposed inhibition mechanism would not require a polysaccharide bridge between HCII and thrombin, therefore, would not so dependent on GAG chain length. We have reported that DS is the preponderant anticoagulant GAG present in arterial wall. However, we found a similar thrombin inhibitory activity of purified aortic DS when compared to the aortic chondroitin sulfate (CS) + DS mixture, on a weight-to-weight basis. CS was removed from the mixture by digestion with chondroitin AC lyase (Chase AC), but simultaneously this enzyme produced a decrease in the DS anticoagulant activity. We also extracted DS from aorta adventitia layer, which correspond more than 90% in the total GAG content. After digestion with Chase AC we observed a decrease of the molecular size of DS, from ~ 30 to 20 kDa, and a simultaneously 5 fold decrease in the anticoagulant activity of the adventitia DS. Overall, these results indicate that slight change in the molecular size of DS modifies significantly the anticoagulant activity of this GAG. This suggests a template-like effect in the HCII-mediated anticoagulant activity of DS.