Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. For nine mRNAs, expression levels in individual piglets were analyzed by NB. These analysis confirmed the array data. In addition, NB analysis showed that one piglet slaughtered at 12 hpi responded quite similarly to rotavirus infection as both 18h piglets did, whereas its 12-h replicate did not, despite the fact that this latter piglet also showed an IFN-c mRNA response. In addition, 7 out of the 12 genes differentially expressed at 12 hpi also reacted at 18 hpi. These results indicated that three out of four infected piglets responded quite analogously. Because we used a limited number of germ-free piglets per time point and measured responses in a mixed population of cells, we imposed stringent criteria for selection of genes ([3.6-fold up-or down-regulation and a false-discovery ratio of less than 5%). Using this approach, we minimized the chance of selecting genes hybridizing differentially solely due to inter-animal variation in gene expression and/or cell composition. However, such stringent selection criteria could have excluded the detection of more rotavirus-regulated genes, especially of genes regulated exclusively in specific types of cells that are present in low quantities in the jejunal mucosa. The different responsiveness of one of the 12-h piglets, however, obliged us to interpret our overall results carefully, especially, concerning the five genes that reacted solely at 12 hpi (TXN, FRK, DppC-2, IF144, and ACTB; see Table 2 ). Nevertheless, data mining revealed relevant relationships between these five genes, 18 h response genes, and processes known to be important for rotavirus pathogenesis.