Metals are widely used in modern medicine: iron, copper, zinc, vanadium, titanium – all of them are vital for treatment of different diseases. Recently a new field of medical technology has emerged, which focuses on the biomedical application of metallic nanoparticles, with a particular interest in a gold and silver-based materials. These structures are already used for photothermal anticancer therapy, drug delivery, bioimaging, radiosensitizers and as drugs themselves. Despite the wide usage of nanoparticles, we still don’t know much about the toxicity of nanomaterials. Nanotoxicological studies are mainly carried out in vitro, but in vivo effects are still elusive. Hence, we focused on the reproductive toxicity of gold and silver nanosized particles. Spherical 10–15 nm gold and silver nanoparticles were synthesized through the reduction of sodium tetrachloroaurate (III) and silver nitrate respectively with ascorbic acid in the presence of sodium polyphosphate as a coating and stabilizing agent. Next, these particles were administered intraperitoneally to the young and adult animals (1- and 6-months old respectively) at 1 mg/kg dose for 10 days. As quantitative markers of functional activity, we used the diameter of epididymal tubules, height and the nuclear cross-section of epididymal epitheliocytes and relative volume of the prostatic epithelium. We showed that intraperitoneal administrations of nanogold to young animals caused no significant histological changes, although we found a decrease in the nuclear cross-sectional area of epididymal epitheliocytes. At the same time, nanogold caused more morphometric changes in adult animals. Similar results were obtained from the nanosilver groups. Silver nanoparticles caused an observable decrease of sperm quantity in the lumen of epididymal tubules with a simultaneous increase in the number of extraepididymal cells in young animals. Morphometric parameters of the epididymis and prostate also decreased. Administration of nanosilver to adult animals also downregulated the morpho-functional state of both organs, although no histological changes were found. We showed that both nanogold and nanosilver can cause adverse effects on the functional activity of the epididymis and prostate of rats. It is worth mentioning that silver nanoparticles were generally more toxic than the gold ones, which correlates with their known mechanism of cellular action. Although the exact mechanisms of gold and silver action require further study, our results are useful for practical usage of nanomaterials in biomedical and clinical practice.