The objective of this study was to use Fourier Transform Infrared (FTIR) spectroscopy and Scanning Electron Microscopy (SEM) to assess whether Nd:YAG laser irradiation associated with a dye or not alters the chemical constitution of the enamel. Fourteen enamel sections were randomly divided into two groups: (1) Nd:YAG and (2) dye + Nd:YAG. First, the untreated enamel surfaces were analyzed by FTIR to acquire the control absorption spectrum. Next, Group 2 received a layer of inactivated coal diluted in deionized water before laser treatment. Enamel samples belonging to groups 1 and 2 were then irradiated with a 1,064-nm Nd:YAG laser (80 mJ, 10 Hz) in the contact mode; the carbonate absorption band and the water absorption band were measured in each sample after irradiation. The water band was measured again 24 h, 48 h, and 7 days after irradiation. Group 1 had statistically similar water and carbonate contents before and after irradiation. Group 2 displayed significantly lower (p < 0.05) water content after irradiation, which remained constant along time at 24 and 48 h. After 7 days, the water content increased slightly, being statistically higher than in the other experimental periods, except for the control. The carbonate/phosphate ratio was measured only at the beginning, and after irradiation, it decreased only in Group 2 indicating carbonate loss (p < 0.05). Irradiation with 1,064-nm Nd:YAG laser associated with a dye reduces the carbonate and structural water content in the enamel.