The research was performed on male Wistar rats based on assumptions that new microelement preparations containing metal nanoparticles and their agglomerates had potential. Morphological and functional changes in tissues in the injection site and dynamics of chemical element metabolism (25 indicators) in body were assessed after repeated intramuscular injections (total, 7) with preparation containing agglomerate of iron nanoparticles. As a result, iron depot was formed in myosymplasts of injection sites. The quantity of muscle fibers having positive Perls' stain increased with increasing number of injections. However, the concentration of the most chemical elements and iron significantly decreased in the whole skeletal muscle system (injection sites are not included). Consequently, it increased up to the control level after the sixth and the seventh injections. Among the studied organs (liver, kidneys, and spleen), Caspase-3 expression was revealed only in spleen. The expression had a direct dependence on the number of injections. Processes of iron elimination from preparation containing nanoparticles and their agglomerates had different intensity.