Holtzman rats of both sexes were fed one of the following semisynthetic diets: 25% protein (control), 10% protein (slight malnutrition), 5% protein (medium malnutrition), and 2% protein (severe malnutrition). The skulls were cleaned and disarticulated with papain; they were defatted, dried, and the total weight (Tw) of each bone was determined. A gravimetric method of estimating bone protein-mineral ratio was performed. Following a decalcification with EDTA, the protein matrix was weighed (PMw). A protein-mineral index (PMI) was defined as: PMI = 100 (Tw-PMw)/Tw. The nutritional deficiencies imposed affected the protein and/or mineral contents of the bones according to three different patterns. The first pattern was followed by the bones of the vault and the facial region. The second one included the basicranial bones. The third one comprised the incisors. These patterns were associated with the histogenetic characteristics of the bones and teeth. A relationship between these findings and previously ascertained functional craniofacial variations in malnourished rats was found. From the differential behavior of the base, the vault, the masticatory apparatus and the incisors, it was inferred that each of these functional cranial components reacted to the experimentally unbalanced nutrition, according to a specific kind of adaptive mechanism.