The amount of fluoride found in the bone is usually correlated with the amount of fluoride found either in water or in a person’s diet. The purpose of this study was to evaluate the beneficial incorporation of fluoride into rat bone after prenatal fluoride administration, using microstructural analysis. Fifteen 8- week-old female were divided into five groups (one control group and four experimental groups), with three rats in each group. During the mating period, pure redistilled water (containing no fluoride) was given to the control group, and redistilled water containing 1/10/20/100 ppm sodium fluoride was given to the experimental groups. The drinking water was prepared by dissolving 2.2 mg NaF (Yakuri Pure Chemicals Ltd., Osaka, Japan) per liter of redistilled water. Rats were sacrificed 4 weeks after their delivery, and their femurs were extracted. X-ray diffraction (XRD; electromagnetic waves) and Fourier transform infrared spectroscopy (FTIR) were performed. The change in the hydroxyapatite structure to fluoroapatite was not confirmed by XRD, and FTIR showed that the inorganic element bands (carbonate, phosphate, and amide band) seemed to be slightly higher in the 20 ppm group, suggesting that the prenatal fluoride treatment through the incorporation of fluoride ions into the hydroxyapatite crystals affected the unit cell size and the bone microstructure.