The effect of K+ and Na+ on the properties of DNA aptamers that selective binds to fibrinogen (FIBRI) and heparin (HEPA) exosites of human alpha-thrombin was studied by circular dichroism (CD). The complexes of FIBRI-K+ were slightly more stable than HEPA-K+. However, lower stability was observed for HEPA-K+ at presence of Na+ in comparison with FIBRI-K+. The analysis of CD melting curves suggests differences in thermal stability of both aptamers at presence of K+. The melting temperatures (Tm) and changes in van't Hoff enthalpy for HEPA-K+ complexes were lower in comparison with those for FIBRI-K+. With increasing HEPA concentration the Tm value increased, but Tm did not change with increasing FIBRI concentration. This suggests formation of HEPA aggregates, while FIBRI aptamers are in monomeric form.