The level of protection conferred by commercial vaccines against the new variant Nebraska 95 isolate was evaluated. Complete protection was observed when the IBV Arkansas vaccine was given and when the Massachusetts-Connecticut vaccine was given at 1 and at 1 and 10 days of age. However, partial protection was observed when the Massachusetts-Connecticut vaccine was given only at 10 days of age. The persistence of IBV Arkansas and Massachusetts vaccine strains in broilers was evaluated. By RT-PCR assay, when given as a single vaccine, the Massachusetts vaccine persisted longer in the tracheas than the Arkansas vaccine. However, only the Arkansas vaccine persisted in cecal tonsils. When the bivalent vaccine was given, the presence of the Arkansas serotype was observed at later ages when compared with the Massachusetts serotype. By the in situ hybridization assay, when the bivalent vaccine was given, IBV persisted longer in the cecal tonsils than in trachea.