To understand the host-parasite relationship during coccidiosis it is necessary to identify the transcriptional profile of the local host. In this study, gene profiling in the mouse jejunum due to infection with Eimeria papillata was investigated using Agilent microarray technology. On day 5 post-infection, the characterization of infected and non-infected mice jejunum transcriptional response was compared. There was an increase in the level of tumour necrosis factor-α, nitrite/nitrate and nitric oxide synthase activity was observed following infection. Also, the activity of glutathione peroxidase was reduced from 86.5 to 38.2 mU/g. In addition, E. papillata infection was associated with an increase in the activities of both the mice alkaline phosphatase and lactate dehydrogenase. Moreover, experimental E. papillata infection in mice induced a significant elevation in protein carbonyl content, by about 70%. Agilent genome microarray detected 11 genes whose expression was up-regulated by more than 10-fold, and 30 genes whose expression was down-regulated by a similar amount five days after infection with E. papillata. The expression profiles of the Fas apoptotic inhibitory molecule 3(FAIM3), chemokine (C-X-C motif) receptor 5 (Cxcr5), succinate receptor 1 (SUCNR1), hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 3 (Hsd3b3) and cytochrome P450, family 2, subfamily b, polypeptide 9 (Cyp2b9) genes, arbitrarily selected from the microarray analysis, closely resemble the expressions determined by quantitative PCR. The data indicate that, E. papillata is associated with the induction of inflammatory response and with gene regulation in mice jejunum.