Objective To investigate genetic stability of P3 strain of Vero cell derived inactivated Japanese encephalitis vaccine.Methods The nucleotide and amino acid sequences of E protein of Japanese encephalitis virus (JEV) P3 strain at different culture period including the mouse brain one passage seed,master seed,working seed the vaccine lot in addition to its 5 passages lot were determined,while the E gene and protein sequences were compared with JEV wide stain (AF036919) from the GenBank.Furthermore,the master seed,working seed,vaccine lot and its 5 passages lot of P3 stain were determined for virus titer,antigen concentration and the vaccine potency.Results The E gene and protein sequences of the above 5 passages of vaccine strain prepared for JEV vaccine showed no difference with homologies of 100％.When the 5 passages of vaccine stain compared with those JEV wide stain (AF036919),the gene sequence at E9,E10,E324,E330,E1223,E1338 showed difference with homologies of 99.73％.No silent mutation were investigated except the amino acid mutation at aE408 (L→S) but was no virulence-associated sites with homologies of 99.80％.The virus titers of the master seed,working seed,vaccine lot and its 5 passages lot of P3 stain were higher than 8.0 lgLD50/ml,while the antigen concentrations and the vaccine potency showed no difference.Conclusion The virus seed bank of P3 strain for Vero cell derived inactivated Japanese encephalitis vaccine showed high genetic stable.