The chicken major histocompatibility complex (MHC) B locus has been linked to resistance to infectious diseases. We have previously provided evidence that the MHC congenic chicken lines 331/B2 and 335/B19 differ in susceptibility to infectious bronchitis virus (IBV) strains M41 and ArkDPI in in vivo challenge experiments. Innate immune responses can be difficult to measure in vivo because they are nonspecific and can be triggered by environmental factors. In an attempt to address this issue, we used tracheal organ cultures derived from 331/B2 and 335/B19 birds to study local cytokine production after in vitro challenge with IBV M41. Interferon (IFN)-β, interleukin (IL)-1β, IL-6, and IL-10 gene expression and production were assessed. Tracheal organ cultures derived from 335/B19 birds presented an increased inflammatory response compared to 331/B2. However, it was not possible to discriminate between cytokine responses in IBV-infected and phosphate-buffered saline–treated tracheal organ cultures. Because tracheal processing entails physical damage to the trachea, it is possible that the tracheal organ cultures presented high levels of inflammation regardless of the IBV challenge. To demonstrate the effects of IBV on innate immune responses in the MHC congenic chicken lines, we performed an additional in vivo experiment that focused on cytokine gene expression and production in tracheas up to 60 hr after a challenge with IBV M41. Our results corroborate previous in vivo observations that suggest that detrimental local inflammatory responses in 335/B19 birds might be associated with their susceptibility to IBV and that inflammation does not necessarily lead to the assembly of an appropriate adaptive immune response. This work provides further insight into the increased susceptibility of 335/B19 birds to infectious bronchitis.