Peroxynitrite is a potent oxidant to nitrate tyrosine of protein, induce DNA strand breaks and promote the lipid peroxidation in vivo, which can result in serious diseases, such as cardiopathy, neurodegenerative disorders and even cancer. However, carbon dioxide can react with peroxynitrite and change the toxicological properties of peroxynitrite, which is in equilibrium with bicarbonate anion in the extracellular milieu (25 mM in plasma). Due to reaction mechanisms of peroxynitrite with amino acids are the bases to explore the damage of protein induced by peroxynitrite. Here, by using stopped flow instrument, UV-visible spectra, fluorescence spectroscopy and high performance liquid chromatography, we investigated the kinetics reaction of carbon dioxide and peroxynitrite in the different environment and the effects of carbon dioxide on damage of amino acids caused by peroxynitrite. The results showed when the temperature was 37°C and pH 7.4, two-order rate constant of peroxynitrite react with NaHCO3 was 2.3×103 M-1·s-1. The damage of amino acids aroused by peroxynitrite was weakened in 0.1 M phosphate buffer solution with 25 mM NaHCO3 and the damage inhibition ratio of tryptophan and tyrosine reached to 27% and 50%, respectively. Moreover, carbon dioxide could also reduce the fluorescence quenching of tyrosine induced by peroxynitrite.