The method for the analysis of cholera toxin gene in V. cholerae strains was developed on the basis of polymerase chain reaction (PCR). This specific and highly sensitive method using primers affecting the site of the DNA of the operon of cholera toxin gene made it possible to identify one copy of V. cholerae genome. For the first time the content of cholera toxin gene in 4 V. cholerae (eltor) strains, obtained from the clinical material of cholera patients in Tajikistan and Dagestan, was shown with the use of PCR.