Foot-and-mouth disease virus (FMDV) has a dual capacity to induce either acute or persistent infection in host animals. Establishment of an in vitro cell model of FMDV persistent infection facilitates the study of the mechanism underlying this type of infection. In this study, we analyzed gene expression profiles of both acute and persistent infections using cross-species microarrays. Our data suggest that human microarrays are more efficient than mouse microarrays in hybridization with cDNA from BHK-21 cells although the mouse is closer to the Syrian hamster in taxonomy. A set of differentially expressed genes (DEGs) that may be involved in the determination of acute or persistent infection was identified by using human or mouse microarrays. Seven common DEGs were found in both human and mouse arrays and showed similar fold changes. Among the DEGs, 33 genes were selected for further validation by using qRT-PCR and presented consistent results. The analysis of Gene Ontology Biological Processes indicated that various biosynthetic and metabolic processes were negatively regulated in the group of acute infection whereas multicellular organismal development processes were positively regulated in the group of persistent infection. Our study demonstrates the plausibility and utility of using cross-species microarrays to study FMDV-infected mammalian cells. The combined use of two types of microarrays can be more informative in exploring the mechanisms underlying the infections of FMDV.