This paper reports hepatitis C virus (HCV) prevalence, genotypes and phylogenetic characteristics in 95 haemophilic Tunisian patients. The studied population included 3 groups of patients according to their date of birth: before 1985 when inactivation procedures for clotting factors was introduced, between 1985 and 1994 when systematic anti-HCV screening of Tunisian blood donors was introduced and after this date. HCV infection was assessed by serological and molecular commercial tests. Genotypes were determined using the INNO-LiPA HCV test and by partial sequencing in the NS5b genomic region. Phylogenetic analyses were performed by comparing NS5b sequences of Tunisian haemophiliacs to published sequences. HCV infection was detected in 50.5% of cases with a significant decrease according to age. Subtype la was the most prevalent followed by subtype 1b (52.6% vs 44.7%); it was more frequent among haemophiliacs born before 1985. NS5b sequences were different from those obtained from non-haemophilic Tunisian patients and showed nucleic affiliation with HCV isolates from the USA. These findings suggest an infection through clotting factors imported to Tunisia and frequently manufactured from US blood donors. In contrast, subtype 1b showed approximately the same distribution among patients born before and after 1985; NS5b sequences from haemophiliacs were randomly distributed among other Tunisian sequences, favouring a transmission through cryoprecipitates prepared from Tunisian blood donors.