Abstract: The rates of infection, the major risk factors for the HCV infection and the distribution frequency of HCV genotypes evaluated among anti-HCV positive haemophiliacs and thalassemics in Iran. Nested RT-PCR used for detection of HCV infection among anti-HCV positive patients. The genotypes of viruses analyzed via Linear Probe Assay (LiPA) method. Sixty percent of the anti-HCV positive haemophiliacs and 50% of the anti-HCV positive thalassemics were HCV infected. Blood clotting factors injection rates in hemophiliacs and the first injection time in thalassemics determined as the main risk factors in HCV infection. Genotyping analysis showed type-1 in 62.5% of hemophiliacs and 87.5% of thalassemics, type 3a in 40.62% of hemophiliacs and 25% of thalassemics and type 6a in one of the haemophiliacs. A total of 9.37% of haemophiliacs and 37.5% of thalassemics were infected with mixed types. The first injection time and the rate of injection determined as the main risk factors in HCV infection. The predominant types of HCV were type 1 and 3a which is similar to the results from the other areas in Iran. Also we detected the type 6a which is not a common type in Iran and not seen in the previous studies.