The goal of this article was to compare the effects of a prolonged use of organic and transgenic soy on the lipid profile and ovary and uterus morphology. Wistar rats were fed three different diets from weaning until sacrifice at 15 months of age. The three diets were: casein-based diet control group (CG), organic soy-based diet group (OSG), or transgenic soy-based diet group (GMSG). There were no differences in food consumption or in the diet isoflavone components among the groups. Compared with the CG diet, both the OSG and GMSG diets were associated with significant reductions in body weight, serum triglycerides, and cholesterol (P < 0.05) (CG = 406 +/- 23.1; 104.3 +/- 13.2; 119.9 +/- 7.3 GMSG = 368 +/- 17.6; 60.3 +/- 4.6; 83.3 +/- 5.7 OSG = 389 +/- 23.5; 72.3 +/- 12.5; 95.5 +/- 8.0, respectively). The volume density of endometrial glandular epithelium was greater in the GMSG group (29.5 +/- 7.17, P < 0.001) when compared with the CG (18.5 +/- 7.4) and OSG (20.3 +/- 10.6) groups. The length density of endometrial glandular epithelium was shorter in both GMSG (567.6 +/- 41.1) and OSG (514.8 +/- 144.5) diets compared with the CG (P < 0.05) diet. GMSG also resulted in reduced follicle number and increased corpus luteum number compared to the OSG or CG diets (P < 0.05). In summary, both GMSG and OSG diets resulted in decreased body weight and lower serum triglyceride and cholesterol levels, and alterations in uterine and ovarian morphology were also observed. The prolonged use of soy-based diets and their relation to reproductive health warrants further investigation.