The HCV genotype can be determined by PCR using nested primers to structural or non-structural HCV regions, followed by hybridization analysis of the amplified products. In this study, two different systems, both based on PCR and hybridization analysis, were used to determine HCV genotype in 32 HCV positive patients at the Clinic of Infectious Diseases, University of Chieti. The main difference between these commercially available systems lies in the different PCR target. Amplification of PCR targets was obtained from all samples. Hybridization analysis gave unequivocal results for all samples with both methods, yielding a 100% rate of genotype determination, with a complete correlation at the genotype level. A lower concordance at subtype level (65% concordance) was found, due only to two types of discrepancies. Both methods proved easy to use in our hands, adding evidence to their potential usefulness and reliability in clinical settings.