Xenograft rejection poses the largest obstacle to successful xenotransplantation. Recent studies have demonstrated that miRNAs play essential roles in embryogenesis, cell proliferation, and pathogenesis of human diseases. However, the role of miRNA in regulating xenograft rejection is relatively unknown. This study was undertaken to analyze the profile of intragraft miRNA expression in a heterotopic mouse-to-rat cardiac xenotransplantation model. Using microarray analysis, a total of 579 miRNAs were detected in the grafts following transplantation. When compared with syngeneic heart grafts, 24 and 25 miRNAs were found to differentially express in xenografts at 24 and 40 hours (endpoint of rejection), respectively, following transplantation. Three major miRNAs were then further analyzed, and it was found that the xenografts showed high expression of miR-146a and miR-155, but low expression of miR-451 when compared with isograft controls. This study suggests that miRNAs detected in this model are potentially involved in the xenogeneic immune response and could play an important role in regulating xenograft rejection. © 2013 Wiley Periodicals, Inc. Microsurgery 34:44–50, 2014.