In this study a viral infection of a tissue culture model system was compared to an in vivo infection, which is of importance to gauge the utility of the model system. The aim was to characterize early immune responses induced by avian influenza virus using tracheal organ cultures (TOC) as a model system. First, the in vitro system was optimized to ensure that the host transcription responses were only influenced by virus infection and not by differences in viral load. Upper and lower trachea both could be used in the cultures because the virus load was the same. Cilia motility was not affected in non-infected TOC and only slightly in infected TOC at 24h post-inoculation. Gene expression profiles of early immune responses were analyzed in in vitro infected TOC, and were compared to the responses found in in vivo infected trachea. The gene expression profile in infected TOC suggested the up regulation of innate anti-viral responses that were triggered by attachment, entry and uptake of virus leading to several signalling cascades including NF-kappaB regulation. Genes associated with IFN mediated responses were mainly type I IFN related. Overlapping gene expression profiles between non-infected and infected TOC suggested that tissue damage during excision induced wound healing responses that masked early host responses to the virus. These responses were confirmed by real-time quantitative RT-PCR showing up regulation of IL-1beta and IL-6. Microarray analysis showed that gene expression profiles of infected and non-infected TOC had a large overlap. This overlap contained many immune-related genes associated with inflammatory responses, apoptosis and immune system process and development. Infected TOC and in vivo infected trachea shared few significantly differentially expressed genes. The gene expression profile of infected TOC contained fewer genes which were expressed at reduced amplitude of change. Genes that were common between TOC and trachea were associated with early immune responses likely triggered by virus attachment and entry. Most of the genes were associated with IFN-mediated responses, mainly type I IFN related. Our study implicates that although the TOC model is suitable for culturing of virus and lectin or virus binding studies, it is not suitable for measuring early immune responses upon viral infection at host transcriptional level.