Technical Abstract: Most soy foods contain isoflavones which under certain conditions may have estrogen-like actions. We have studied the effects of soy protein isolate (SPI) on bone quality and compared these effects to 17 ß-estradiol (E2). Weanling male and female rats were either fed a SPI-containing diet, or administrated three doses of E2 (0.1, 1, 10 µg/kg/d), or received combination of SPI diet and E2 10 µg/kg/d for 14 days beginning on postnatal day 17. In long bones from both sexes, only trabecular bone mineral density (BMD) was increased in SPI-fed rats as compared to control casein-fed animals (p < 0.05). In sharp contrast, 10 µg/kg/d E2 not only increased trabecular BMD, but also cortical BMD compared to casein controls (p<0.05). Rats treated with the combination of SPI and E2 had an intermediate bone effect. Microarray analysis revealed 652 genes regulated by SPI diet, 491 genes regulated by E2, and 266 genes regulated by both SPI diet and E2 compared to casein control diet. In particular, the gene expression of caveolin-1, a known protein localized in cell membrane which conveys non-genomic action, was down-regulated (p<0.05) in rats fed soy, but not by E2 compare to casein control diet. Activating transcription factor 3 was only up-regulated (p<0.05) by E2. These results indicate significant non-classical estrogenic stimulation of trabecular bone formation associated with SPI consumption in early development.