Extracellular matrices isolated from several mammalian organs/tissues have found several clinical uses as xenografts or implants. However, they may cause complications because of adverse immunologic reactions. Scaffolds that promote favorable graft-acceptance reaction are preferred for fabricating xenografts. The objective of this study was to evaluate the immunogenic potential of a porcine cholecyst-derived scaffold (CDS), prepared by a non-detergent/enzymatic method, in comparison with jejunum and urinary bladder-derived scaffolds in a rat subcutaneous model. Key graft-rejection/acceptance reaction was evaluated at the site of implantation by studying the occurrence and/or function of immunocompetent cells in the tissue reaction. There was differential occurrence of M1-macrophage, M2-macrophage, T-helper cells, T-cytotoxic cells, B-cells, and mast cells in the tissue reaction and the CDS attracted few cells compared with other scaffolds. Real-time polymerase chain reaction for evaluating mRNA of functional markers like inducible nitric oxide synthase (M1 macrophage), arginase 1 (M2 macrophage), interferon gamma (TH1 lymphocytes), and interlukin-4 (TH2 lymphocytes) suggested that the CDS, compared with the scaffolds prepared from small intestine and urinary bladder, elicited M2 macrophage and TH2 lymphocyte polarization that are congenial graft-acceptance reactions. The results indicated that CDS has less immunogenic potential compared with the scaffolds prepared from jejunum and urinary bladder when used as subcutaneous graft in rats. It was concluded that CDS is a promising animal-derived xenograft for biomedical application.