The purpose of this study was to determine hepatitis C virus (HCV) genotypes and their relationship to HCV RNA levels over time in a cohort of multitransfused hemophiliacs. Following reverse transcription and polymerase chain reaction amplification of HCV RNA, the product DNAs were genotyped by using the line probe assay. HCV RNA was quantified by the branched-chain DNA assay. Genotyping was done on 109 serum samples from 32 subjects. Genotype 3a had the highest prevalence (41%), followed by genotypes 1a (31%) and 1b (13%). Changes in genotypes were observed in 18 (58%) of the subjects >3-15 years of age. Changes were more common in human immunodeficiency virus (HIV)-positive subjects (13/17) than in HIV-negative subjects (5/15) (P=.014). HCV RNA increased 30-fold in HIV-positive subjects whose genotypes changed. Consensus nucleotide sequencing confirmed genotype changes in 2 patients. We conclude that genotype changes are common in hemophiliacs with chronic HCV, particularly in those who are coinfected with HIV.