Introduction and aim of work: thyroid hormone is known to play a critical role in the development and growth of the testis. So, this study was designed to compare between the effect of transient and persistent neonatal hypothyroidism on the testis of adult rats. Material and Methods: Thirty newborn rats (1 day old) were classified equally into control group and two experimental groups. In experimental group I, the transient hypothyroidism was induced in neonates by giving their lactating mothers 0.05%, 6-propyl-2 thiouracil (PTU) through drinking water for 30 days after birth then the treatment was withdrawal for 60 days. In experimental group II, the persistent hypothyroidism was induced by giving the neonates 0.05% PTU through their mother milk until weaning then directly through drinking water for 90 days after birth. After 90 days postpartum, all animals were anaesthetized and their testes were dissected out and processed for light and electron microscope examination. Results: In experimental group I, the testes of transient hypothyroid rats appeared with large seminiferous tubules (ST) that the length of their diameters and the height of their lining epithelium were significantly increased as compared to those of control rats. They were lined by many Sertoli cells, primary spermatocytes, secondary spermatocytes, early spermatides and late spermatids. The interstitial spaces contained some Leydig cells and few fluid. In experimental group II, the testes of persistent hypothyroid rats appeared with small ST that the length of their diameters and the height of their lining epithelium were significantly decreased as compared to those of control rats. They were lined by thin disorganized germinal epithelium containing many Sertoli cells and few germ cells. Many sloughed degenerating cells and large multinucleated giant cells were seen in the lumen of ST. The interstitial spaces contained many connective tissue cells, congested blood vessels, excessive collagen fibers and abundant fluid. Electron microscope examination, revealed Sertoli cells which were surrounded by wide spaces due to loss of germ cells. They contained distorted mitochondria, nuclei with peripheral heterochromatin condensation and free processes due to loss of tight junction between them. In conclusion, the present study revealed that the neonatal transient hypothyroidism enhanced the growth of the testes that they contained large seminiferous tubules with many germ cells. While, the persistent hypothyroidism induced testicular atrophy with degeneration of germ cells. So, estimation of thyroid hormone level is recommended in all neonates immediately after birth for early diagnosis and treatment of thyroid hormone deficiency to prevent serious adverse effect of hypothyroidism on the testis.