The mechanism by which the foot-and-mouth disease virus (FMDV) initiates infection of cells is thought to involve the attachment of the viral capsid to host integrins on the surface of target cells. However, the role of integrins in FMDV infection still needs to be fully understood, although it has been demonstrated that integrin αvβ6 interferes with FMDV in vitro and results in neutralization of its infectivity. In the present study, we describe the cloning and sequencing of suckling mouse integrin β6 and the subsequent expression of two segments of integrin β6 extracellular domains: β6-1 (which contains the ligand-binding domain) and β6-2. Sequencing of the mouse integrin β6 subunit revealed close homology (~90%) with its human counterpart. When recombinant integrin extracellular domains β6-1 and β6-2 formulated with adjuvant were inoculated into guinea pigs, anti-integrin antibody expression was high before FMDV challenge. Interestingly, guinea pigs (50%) inoculated with integrin β6-1 were protected from FMDV infection; in contrast, none of the animals inoculated with integrin β6-2 were protected. This result indicates that an integrin blockade may be able to interfere with FMDV infection in vivo, which raises the possibility that targeting integrin in vivo may be the basis for a new strategy to control FMDV infection.