The aims of this study were to determine the functional biocompatibility of low concentration-SDS-decellularised porcine aortic roots in vivo. A previously developed process was modified for 9 and 15 mm diameter aortic roots to facilitate implantation into the porcine abdominal aorta (n=3) and juvenile sheep right ventricular outflow tract (n=7), respectively. Native allogeneic aortic roots were used as controls. Acellular porcine roots explanted from pigs at 6 weeks were largely repopulated with stromal cells of appropriate phenotype, and there was evidence that macrophages were involved in the regenerative process. Native allogeneic roots were subject to a classic allograft rejection response. Acellular porcine roots explanted from sheep at 6 months showed evidence of appropriate cellular repopulation, again with evidence of a role for macrophages in the regenerative process. There was some degree of calcification of two of the explanted acellular roots, likely due to incomplete removal of DNA prior to implantation. Native allogeneic ovine roots were subject to a classic allograft rejection response involving T-cells which resulted in overtly calcified and damaged tissues. The study highlighted (1) the importance of removal of DNA from acellular porcine valved roots to avoid calcification and (2) a role for macrophages in the regeneration of low concentration SDS decellularised aortic roots, as has been reported for other acellular biological extracellular matrix scaffolds.