Animal tissues are extensively used as scaffolds for tissue engineering and regenerative therapies. They are typically subjected to decellularization process to obtain a cell-free extracellular matrix (ECM) scaffolds. It is important to identify chemical structure of the ECM scaffolds and Fourier transform infrared (FTIR) appears to be a technique of choice. In this chapter, FTIR spectra of native and decellularized buffalo aortae, buffalo diaphragms, goat skin, and native bovine cortical bone are presented. The transmittance peaks are that of organic collagen amide A, amide B, amide I, amide II and amide III chemical functional groups in both native and decellularized aortae, diaphragms and skin. In bone, the transmittance peaks are that of inorganic ν1, ν3 PO43−, OH− in addition to organic collagen amide A, amide B, amide I, amide II and amide III chemical functional groups. These important transmittance peaks of the tissue samples will help researchers in defining the chemical structure of these animal tissues.