Protein energy malnutrition has become a major health issue in developing countries. In the present study, the effect of protein deficiency on the small intestine and liver tissue content of macroelements and trace elements was investigated in weanling rats. Forty-five male weanling Wistar albino rats were divided into three groups. The control group (C) was fed a standard diet containing 25% casein, whereas the two experimental groups E1 and E2 consumed 12% and 3% casein, respectively, over a period of 45 d. The tissue samples were analyzed for zinc, copper, iron, manganese, calcium, and magnesium by atomic absorption spectroscopy. The protein-deficient groups showed increased levels of iron in both tissues and decreased manganese in small intestine tissue from the E1 group. No other differences were found for the other elements. These results suggest that protein deficiency might cause iron accumulation in the liver and intestine and decreases of manganese in the small intestine.