Abstract A new water-insoluble precipitate was obtained by mixing chitosan with sodium carboxymethylcellulose, an anti-thrombogenic agent. The mole ratio of N/COO− in the polyelectrolyte complexes was estimated to be 0.3935–0.9071. It was found that pH, mole ratio of N/Na in the reaction mixture and the order of mixing play an important role in determining the composition ratio of N/COO−. In order to clarify the relationship between the molecular conformation of the polyelectrolyte complexes and their properties, IR spectroscopic studies, elementary analyses, color reaction with Toluidine Blue, studies on solubility and blood clotting test in vitro were performed. The polyelectrolyte complex, prepared at higher pH, differed from that prepared at lower pH, particularly in the density of –COOH group site. These results were interpreted in terms of the variation in the degree of electrolytic dissociation of the weak polyelectrolytes, caused by pH change. All the polyelectrolyte complexes revealed clot-inhibition in vitro. The clot-inhibiting behavior seems to be due to the clot-inhibiting surface of the polyelectrolyte complex, not to the elution of the activity from the surface.