Permanent and deciduous human teeth treated by a dental Er‐doped yttrium‐aluminium‐garnet pulse laser (λ = 2940 nm) as well as by classical drilling tools under conditions typical of the clinical practice were studied by ultraviolet Raman and Fourier transform infrared (FTIR) reflection microspectroscopy. Enamel was analyzed by both spectroscopic methods, whereas dentine was studied only by FTIR reflection because of the high level of photoluminescence continuum background even when a wavelength of 325 nm was used in inelastic light scattering experiments. The applied energy and pulse frequency of the dental laser varied between 200 and 500 mJ and between 10 and 30 Hz, respectively. The most important result is that after the laser treatment, the hydroxyapatite structure in both permanent and deciduous enamel is preserved: the apatite Ca‐P‐O framework remains intact, and the content of channel OH‐ groups is not changed within experimental uncertainties. The calcium‐phosphate framework of dentine also exhibits negligible laser‐induced changes. The only alterations in enamel induced by laser as well as by mechanical drilling are reduction of the amount of CO32‐ in apatite and changes in the protein conformation. The laser impact on the organic material and carbonate groups is strongest for laser power of 8 W; for powers of 4 or 5 W, the combination of higher pulse energy and lower pulse frequency has less impact than the combination of lower energy and higher frequency. No differences between deciduous and permanent teeth in their resistivity to laser irradiation with λ = 2940 nm were detected. Copyright © 2013 John Wiley & Sons, Ltd.