This study aimed to assess the morphological changes in neonate vitrified testicular grafts after host treatment with melatonin. Neonate vitrified testes, candidates for transplantation to treated and nontreated groups receiving melatonin, were thawed in media containing or not containing 100 μm melatonin. Following transplantation, melatonin (20 mg kg−1 per day) and saline were given to the treated and nontreated groups for up to 9 weeks. The testicular status was assayed by terminal deoxynucleotidyl transferase (TdT)-mediated deoxyuridine triphosphate (dUTP)-biotin nick-end labelling TUNEL, semi-thin section and ultra-structure studies. Chi-squared test was used to compare categorical variables between the groups. Overall, the degenerative and apoptosis changes in the vitrified testis parenchyma were not significant. However, atrophic seminiferous cords and jumbled appearance of the interstitial space were more often observed in the nontreated group than in the treated ones. Semi-thin sections showed that the germinal epithelium was taken in a normal arrangement on the testicular grafts of both groups. Nevertheless, ultrastructural analysis revealed that the characteristics of interstitial space cells, basement membrane BM and epithelial cells of seminiferous tubules in the treated group were better than those in the nontreated group. The study revealed a beneficial effect of melatonin on vitrified neonatal testes and after that, on restoring testicular grafts.