Abstract: Objective To investigate the variation of cytotoxic T-lymphocyte (CTL) and neutralizing epitopes in F protein of respiratory syncytial virus (RSV) isolated in Sichuan. Methods Nearly full-length of F protein gene of 10 strains of RSV isolated in Sichuan was amplified by RT-PCR and sequenced. The genetic variations, especially the CTL and neutralizing antibody epitopes within different subtypes and genotypes were analyzed and compared. Results The F protein of RSV is highly conserved within the two subtypes, with the P-distances of nucleotide and amino acids were 0.102±0.005 and 0.058±0.006, respectively. Neutralizing epitopes 47F and L4 were conserved between the subtypes, but RS-348 and 7C2 were only conserved within the subtypes. CTL epitopes HLA B*57,HLA A *01 and HLA Cw*12 were conserved only within subtype A. There were specific different sites between the subtypes. Conclusion The sequences of F protein from Sichuan RSV isolates were highly conserved, so as the epitopes on F-protein within subtypes, the identified CLT epitopes in subtype A may not be recognized in subtype B virus.