Protein malnutrition is a public health problem, and in childhood, it can lead to muscle deficits. Here, our objective was to evaluate the effects of malnutrition upon the muscle fibers in the medial pterygoid and braquial biceps. Ten just weaned rat pups that had been born to parents fed a nourished or malnourished diet (N = 5 per group) were studied. The medial pterygoid and braquial biceps muscles were removed and cross-sectioned, and histological staining with picrosirius and histochemistry reaction with nicotinamide adenine dinucleotide - tetrazolium reductase (NADH-tr) were performed. The samples stained with picrosirius were observed under polarized light, and from the qualitative analysis, we observed that type I collagen fibers were only present in the braquial biceps muscles of the nourished animals. The NADH-tr reaction indicated that the pterygoid muscle specimens from the malnourished pups lacked intermediate muscle fibers. The cross-sectional area of the muscle was lower in the malnourished group than in the nourished group. The density of muscle fibers was higher in the malnourished group than in the nourished group. The consequences of malnutrition were visible when comparing the muscles. We concluded that the differences in daily muscle action along with the differences in embryological origin are instrumental in establishing the results.