To determine whether fistulation and differing strains of Haemonchus contortus complicate genome analysis of the host response to infection, two pilot experiments examined parasite development and gene expression in the abomasal mucosa of parasitised sheep. No significant differentially-expressed genes were detected in a comparison between ivermectin-susceptible McMaster and ivermectin-resistant CAVR strains of H. contortus. This demonstrated that the sheep response was not significantly altered by the ivermectin-resistance status of the parasite. However, sheep infected with McMaster strain had a significantly lower proportion of larvae and a higher mean FEC at post-mortem than sheep infected with CAVR, suggesting that McMaster larvae advance to patency faster than CAVR larvae. Abomasal fistulation resulted in significant upregulation of three genes and significant downregulation of two genes. Fistulated sheep had significantly lower FEC than the other groups but the proportion of larvae at post-mortem was not significantly different to other groups infected with the same strain (CAVR). Hence fistulation does not alter establishment of the CAVR isolate, but may slow its progression to patency. The observation that different H. contortus strains and abomasal fistulation induced minimal changes in mucosal gene expression validated the design of a subsequent experiment (manuscript in preparation) where sequential biopsies taken during infection were analysed by microarray to describe the molecular responses which inhibit larval establishment.