In-office and at-home bleaching techniques are widely used methods for the whitening of teeth. However, the safety of these techniques has not been clarified yet. The aim of the current study is to investigate the in-office- and at-home-bleaching-induced structural and quantitative changes in human enamel and dentin at the molecular level, under in vitro conditions. The Fourier transform mid-infrared (mid-FT-IR) spectroscopic technique was used to monitor bleaching-induced structural changes. Band frequency and intensity values of major absorptions such as amide A, amide I, phosphate (PO4), and carbonate (CO3-2) bands, for treatment groups and control, were measured and compared. The results revealed that both procedures have negligible effects on dentin constituents. In office-bleached enamel, in addition to demineralization, a decrease in protein and polysaccharide concentrations, mineral-to-protein ratio, and the strength of hydrogen bonds around NH groups, as well as a change in protein secondary structure were observed. The protein structure changed front beta-sheet to random coil, which is an indication of protein denaturation. However, no significant variations were observed for at-home bleached enamel. The control, at-home, and in-office bleached enamel samples were differentiated with a high accuracy using cluster analysis based on FT-IR data. This study revealed that office bleaching caused deleterious alterations in the composition and structure of enamel that significantly affected the crystallinity and mineralization of the tissue. Therefore, at-home bleaching seems to be much safer than in-office bleaching in terms of molecular variations.