BACKGROUND: Infectious bronchitis virus (IBV) causes severe economic losses worldwide. IBV has a broad tissue distribution with different viral loads in different tissues. Additionally, IBV can induce apoptosis in infected cells. AIMS: The present study aimed to evaluate the role of the genetic background of chickens in viral load and the expression level of apoptotic genes in different tissues of two hybrids of commercial broiler chickens (Ross 308 and Cobb 500) challenged with IBV. METHODS: Chickens at 21 days of age were nasally challenged with 200 μL of allantoic fluid containing 10 EID/ml of Iranian variant-2-like IBV (IS/1494). The expression level of apoptotic genes (, , , and ) in the tracheal and renal tissues and the amount of viral load in the tracheal, renal, and cloacal swab samples were investigated two, five, and seven days after IBV infection by RT-qPCR assay. RESULTS: The amount of viral load and apoptotic the expression level of apoptotic genes in the tracheal (two and five days after infection) and renal samples (seven days after infection) were significantly higher in the Ross challenged group than in the Cobb challenged group.Furthermore, no difference was observed in the cloaca viral load on sampling days. CONCLUSION: To our knowledge, this is the first report that evaluated the role of the chickens' genetic background in the amount of viral load and the expression level of apoptotic genes against IBV. Further studies are needed to investigate the pathogenic characteristics of IBV in Ross 308 and Cobb 500 chickens.