SUMMARY:The contents of soybean can modify the structure of the reproductive system, especially, when consumed for prolonged periods. In this study, we evaluated the effects of the consumption of transgenic soybean on rat penis morphology after prolonged use. Wistar rats (n = 30) were divided into three groups according to diet: Transgenic Soybean (TS) group, Organic Soybean (OS) group and Control (C) group. After 455 days of intake, the rats were sacrificed and the penises were excised and fixed in formalin for subsequent histological processing. The samples were stained with hematoxylin and eosin, Weigert's resorcin-fuchsin stain, and picrosirius red with polarization. The images were scanned for the histomorphometric analyses of the corpora cavernosa, corpus spongiosum, erectile tissue, and tunica albuginea as well as the measurement of the thickness of the tunica albuginea. The diameter and areas of the penile arteries with the intima and media tunica were also measured. The elastic fibers of the tunica albuginea, corpora cavernosa and corpus spongiosum were quantified using stereological methods. No significant differences were observed in the collagen and elastic components among the groups. We concluded that no statistically significant differences were found among the groups, demonstrating that the prolonged consumption of OS and TS does not affect the penile structure.