Neonatal maternal separation is used to evaluate the effects of early life stress on various systems. The current study evaluated the impact of early life stress exposure on the morphometry and ultrastructure of adult male albino rat testis and clarified its intimate relation with hypothalamic-pituitary-thyroid/Adrenal and gonadal axes. Thirty pregnant rats (dams) were divided into groups (i), (ii) and (iii). Neonates(pups) were also divided into; control (I), and neonatal maternal separation II (NMS II): pups were segregated from their dams for 2 hours /day. Group (NMSIII): pups were segregated from their dams for 4 hours/day from postnatal day 0 to postnatal day 14. Histological results revealed distortion affecting the testicular parenchyma in groups (II) and (III). Sections from both groups revealed markedly disrupted seminiferous tubules; decreased height of germinal epithelium; and decreased tubular diameter with widened interstitium. Immunohistochemical results revealed that the number of proliferating cells (ki67 positive cells) and inducible nitric oxide synthetase (iNOS positive cells) were significantly attenuated in both groups II, III. No substantial change was observed in the quantity of apoptotic cells. Degenerative signs were observed by transmission electron microscopy in both groups II and III; but much more extensive in group III. Sertoli cells, spermatogonia and primary spermatocytes showed irregular nuclear membrane, degenerated mitochondria with distorted crista, dilated endoplasmic reticulum and rarified cytoplasm. Extensive drop in sperm density in epididymal tissue was clearly observed in group III. Biochemical analysis revealed increased serum levels of oxidative stress markers and significant attenuation of different hormones of the Hypothalamic-Pituitary axis in groups II and III.