Defining predictors for insect-transmitted virus (arbovirus) disease cycles requires an understanding of the molecular interactions between the virus and vector insect. Studies of orbiviruses from numerous geographic regions have indicated that virus genes are affected by insect population differences. Therefore, the authors have initiated genetic studies of Culicoides sonorensis, isolating cDNAs for characterisation of differential insect gene expression, as well as a gene discovery project. Previous work identified insect transcripts elevated in orbivirus-infected female midguts at one day post infection (pI). Here, we report cDNAs that were more abundant in midguts two days following an epizootic haemorrhagic disease virus feeding, as well in head/salivary glands at three days pI. Of the cDNAs identified in midguts at two days pI, three encode translational machinery components, and three encode components that affect cellular structural features. Of the differentially expressed salivary gland cDNAs, only one was homologous to a previously identified gene, a putative odorant binding protein.