Infectious bronchitis virus has been recognized as highly contagious disease in chickens. In this study, 138 birds from 10 broiler chicken flocks that suffered from respiratory disease were examined to study the pathological lesions associated with IBV infection in naturally infected flocks. Moreover, the infection was confirmed via virus isolation and PCR. Samples were harvested from both Sharkia and Gharbia provinces during one year (October 2014-2015). The clinical examination of the investigated birds showed nasal discharges, gasping and rales. Congested trachea with lumen contained mucus and caseated material at the biforcation of the two main bronchi were characteristic in most of the necropsied birds. The kidneys were enlarged and dark red or pale with the presence of whitish precipitate in the ureters. Four isolates recovered from four different broilers chicken's flocks were further analyzed by S1 glycoprotein gene sequencing. The phylogenetic analysis of the deduced amino acids sequences of the four strains revealed that they were closely related to the IBV Egyptian variant 2 and IS/1494/2006 strains. The histopathological examination of the kidneys showed focal aggregation of lymphocytes in the renal cortex and the medulla. The liver showed multiple focal areas of necrosis which replaced by lymphocyte and heterophils aggregation. The spleen showed thickened capsule with subcapsular hemorrhage and mild to severe focal depletion of lymphocytes. Trachea, lungs, proventriculus, intestine and bursa showed hyperplasia and degenerative changes in their epithelium. Blood vessels showed endotheliosis with perivascular edema and leukocyte infiltration in various organs. Edema was also seen in heart, trachea and lungs. Finally, it could be concluded that infectious bronchitis virus is a major cause and strongly implicated in respiratory and/or renal problems of the Egyptian broiler chicken flocks. Moreover, Egyptian variant 2 still evolving and causing severe damage to renal tissue and various organs.