An experiment estimating influence of antiviral drug indinavir treatment during pregnancy on bones and teeth development in newborn rats was performed. Two different fluorescence noninvasive spectroscopy techniques, i.e. laser (407 nm)-induced fluorescence method to characterize the organic fluorescent molecules and X-ray fluorescence analysis to determine mineral components were used to study the surface response of femur, mandible and incisor during their formation in the first month of a rat’s life. Differences in autofluorescence depending on the form of the bone were observed on the basis of the emission from enamel in 7-, 14- and 28-day-old newborn rats. The dependence between decrease in intensity of fluorescence and increase in mineralization with age in newborn rats was observed. An enhancement of the autofluorescence and a decrease in the concentration of Ca as a main element, as well as disturbances in the concentration of Zn as trace element were observed for bone as well as teeth in newborns during the first month of their life after maternal administration of indinavir (500 mg kg−1 P.O.) in comparison with the control group. The results indicate that indinavir causes a delay in development of the skeleton and teeth in newborn rats.