Background Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now common, and several tools exist. Results We describe the use of MAPPFinder, a component of GenMAPP to characterise the biological pathways affected in chickens infected with the protozoan parasite Eimeria. Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways. Conclusion GenMAPP/MAPPFinder provides a means to rapidly visualise pathways affected in microarray studies. However, it relies on good genome annotation and having genes reliably linked to pathway objects. We show that GenMAPP/MAPPFinder can produce useful results, and as the annotation of the chicken genome improves, so will the level of information gained.