Collagen is the most abundant protein in humans and animals, comprising of one third of the total proteins that accounts for three quarters of the dry weight skin in humans. Collagen containing a range of proteins has been reported for tissue engineering applications, but, only a small number of studies related to chemical structure evaluation of collagen are found in the literature. Collagen can be obtained from both the natural and synthetic sources and offers a wide range of biomedical applications due to its excellent biocompatibility and low immunogenicity. Hence, it is important to identify chemical structural properties of collagen and Fourier transform infrared (FTIR) appears to be a technique of choice to study their chemical structure. This review aims to highlight the use of FTIR to study collagen-based biomaterials, using it for characterization of collagen extracted from various sources. Characterization of collagen-based materials used in wound healing, skin substitutes, derma fillers, and aging of skin, collagen containing drug delivery agents, collagen-based materials used in tissue engineering, bone regeneration, and osteogenic differentiation is discussed in detail. FTIR analysis of collagen-containing materials used for dental applications, cleft-palate, and in alveolar-ridge preservation has also been highlighted.