The antigen activity of the synthetic fluorescently labeled peptides, overlapping immunoresponsive epitops a.a. 7-19, 20-34 from N-end part and a.a. 73-85 from the central area of the nucleocapsid protein of C hepatitis virus, was tested using the method of fluorescent polarization immunoassay (FPIA) with 40 samples of the blood serum of patients with viral C hepatitis. A comparative study of analytic characteristics of FPIA method was performed, based on the application of synthesized peptides, as well as of the commercial ELISA test system (BEST anti-HCV-test 4, Vector Best Ltd.). The performed research revealed that the developed method has a high specificity and sensitivity level. The comparability of summary FPIA results with the commercial ELISA test system was 85%, which evidences the prospects of further research in this direction. The principal possibility of the application of the polarization fluorescent immunoassay for the determination of antibodies to the nucleocapsid protein of the C hepatitis virus in clinical serum samples was demonstrated.