The aim of this study was to assess the influence of soy isoflavones, administered pre- and later postnatally, on the estrogen receptor α (ERα) and β (ERβ) expression in bones and to examine the mineral metabolism of the skeletal system in male rats. In bones, ERs were examined with an immunohistochemical method; in blood, estradiol with chemiluminescence immunoassay and in blood and bones, calcium and magnesium with atomic absorption spectrometry and fluorides with a potentiometric method were examined. Decreased immunoexpression of ERα and the increased intensity of immunofluorescence of ERβ in osteocytes in the femur of experimental rats were observed. In the serum of treated rats, a significantly higher concentration of estradiol and lower calcium were observed. The content of magnesium and fluoride were significantly higher in the bones of the examined animals. The data presented show that pre- and postnatal supplementation of male rats with soy isoflavones may considerably increase the concentration of estrogens in serum, with a concurrent effect on the mineral composition of bones.