Caffeine is a methylxanthine which permeates the placenta. In studies on animals, it has been shown to produce teratogenic and embryotoxic effects in large doses. The objective of this study was to assess the influence of caffeine on the development of bone tissue, with particular reference to elemental bone composition using an X-ray microprobe. The research was conducted on rats. The fertilized females were randomly divided into an experimental and a control group. The experimental group was given caffeine orally in 30 mg/day doses from the 8th to the 21st day of pregnancy, while the control group was given water. The fetuses were used to assess the growth and mineralization of the skeleton. On the basis of double dyeing, a qualitative analysis of the bone morphology and mineralization was conducted. For calcium and potassium analysis, an X-ray microprobe was used. In 67 fetuses from the experimental group, changes in skeleton staining with the alcian-alizarin method were noticed. The frequency of the development of variants in the experimental group was statistically higher. In the experimental group,a significant decrease in the calcium level, as well as an increase in the potassium level, was observed. The X-ray microprobe's undoubted advantage is that is offers a quick qualitative and quantitative analysis of the elemental composition of the examined samples. Employing this new technique may furnish us with new capabilities when investigating the essence of the pathology process.