Fourier transform infrared (FTIR) spectroscopy is one of the most common vibrational spectroscopic techniques used in biomaterials composition testing. In this chapter, we demonstrated how FTIR can be used for the analysis of the course of foreign body response (FBR) to a phycogenic bone substitute, in mice subcutaneous implantation model. We also examined how addition of blood to the bone substitute influences the FBR course. Natural apatite Algipore was analyzed prior to implantation, and 10 and 30 days after implantation using FTIR spectroscopy. Differences in the IR bands between different groups and time points were noticed in the FTIR spectra. Thirty days after implantation, the IR bands in the region approx. 3,600-1,300 cm−1 were assigned to newly generated protein collagen, which appeared to be more pronounced when biomaterial is combined with blood. Findings obtained by FTIR analysis correlate with our previous findings by other methods, which indicates that FTIR can be used in assessment of biomaterial-mediated tissue response and healing events.