Background: Malnutrition due to protein deficiency is an emerging problem worldwide particularly in the developing countries. Reproductive system development and growth depends on maintaining healthy nutrition especially in childhood and adolescence. The present study aims at studying the possible protective efficacy of carnosine in testicular atrophy, defective spermatogenesis and reduced reproductive performance induced by supplementation of protein deficient diet (PDD) to male rats. Methods: Forty juvenile male albino rats were allocated into four equal groups; each group is 10 rats (i) normal control rats, (ii) protein deficient diet (PDD) group (received PDD for 75 days and saline intraperitoneal (IP) 5 days/week), (iii) carnosine (CAR) group (received carnosine 250 mg/kg body weight (bw), IP 5 days/week for 75 days); (iv) CAR-PDD group (received PDD for 75 days and carnosine 250 mg/kg body weight (bw), IP 5 days/week). Results: PDD supplementation lead to decreased body and testicular weights, reduced sex hormones and sperm count, motility and vitality (Live: Death ratio). In addition, the PDD-treated group had decreased levels of the antioxidant enzymes as reduced catalase (CAT) and glutathione (GSH) levels in testicular tissue. These toxic effects were accompanied by elevation of the pro-inflammatory cytokines, tumor necrosis factor-alpha (TNF-α). Increased proapoptotic marker; caspase-9 and decreased Bcl-2 was also found. On the other hand, CAR co-administration with PDD significantly evaded these effects which were confirmed histologically. Conclusion: CAR could be used as complementary supplements in malnutrition for protection against PDD induced testicular atrophy in male albino rats.