A rat subcutaneous implantation model was used to evaluate the in vivo degradation and tissue response of cholecyst-derived extracellular matrix (CEM). This response was compared to that of glutaraldehyde (GA) cross-linked CEM and porcine heart valve (HV), which are designated as GAxCEM and GAxHV, respectively. Tissue composition, inflammatory cell distribution, and angiogenesis at the implant site were quantified using stereological parameters, thickness (Ta), volume fraction (Vv), surface density (Sv), length density (Lv), and radius of diffusion (Rdiff). CEM was completely infiltrated with host tissue at 21 days and resorbed by 63 days. GAxCEM was also infiltrated with host tissue, while GAxHV matrix was impermeable to host tissue infiltration. Both GAxCEM and GAxHV retained their scaffold integrity until 63 days with no apparent degradation. A fibrous tissue of thickness <52 mum, rich in collagen and vasculature, surrounded all scaffolds, and from 21 to 63 days the fibrous tissue showed maturation with a significant increase in their fibrocyte content. No signs of acute inflammatory response were observed in the study period for any of the scaffolds, while the chronic inflammatory response was predominated with macrophages for all scaffolds except for CEM at 63 days. A higher degree of giant cell formation was observed with GA cross-linked scaffolds. From 21 to 63 days, lymphocytic response decreased for CEM, while it increased significantly for GAxHV. Angiogenesis/neo-vascularization was uniform for CEM (reaching the core), significantly lower for GAxCEM within the implant area as compared to CEM, while restricted to the exterior of GAxHV matrix. In summary, CEM was a fast degrading scaffold that induced a transitional inflammatory response accompanied by gradual resorption and replacement by host connective tissue as compared to the very slow degrading GA cross-linked controls, GAxCEM and GAxHV, which caused a sustained chronic inflammatory response and remained at the site of implantation until the end of the study period of 63 days.