Tracheal swabs and different organs are collected from 17 chicken farms showing respiratory signs and variable mortalities in different governorates. Three successive blind serial passages were performed. Four IBV isolates are detected in vaccinated chickens by RT-PCR and are identified by sequence and phylogenetic analysis of portion of S1 gene. Two IBV isolates, IBV S40 and IBV S61, are related to Mass reference strains (Egypt/F/03, M41, H120, Ma5, and M52). However, IBV S78 and IBV S82 are related to Egyptian variant 2 IBV strains Ck/Eg/BSU- 2/2011 and Ck/Eg/ BSU-3/2011.These results indicate the continuous evolution of Egyptian IBV circulating in chickens despite vaccination using H120 live attenuated vaccine.