Fluoride (F) is an important element for the mineralization of body tissues. The purpose of this study was to administer fluoride prenatally to rats to evaluate its beneficial concentration for rat bone using microstructural analysis, to analyze its effect on the bone structure, and to evaluate the effect of its transfer through rat placenta. Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectrometry (NMR) were performed. The ¹⁹F NMR and ³¹P NMR signals suggested the existence of fluoride ions in the apatite lattice because the signals were caused by the fluoride ions that were coupled to the phosphate atoms and were affected in the phosphate phases other than the element phases in the apatite. Consequently, if it was not affected too much, the desirable concentration of prenatal fluoride treatment could have a helpful effect on the bone crystal structure through placental fluoride transfer.