Adult Holtzman rats were submitted during suckling period to a food restriction with or without protein or carbohydrate restoration. Twenty-one-day-old weanling pups were compared with controls of 9, 13, 17, and 21 days of age. Lateral craniofacial roentgenographies were taken. The length in midsagittal plane of each bone and its angle with respect to the vestibular line were measured in males. In females, the brain and the left masseter muscle were weighed, and the muscle/brain ratios (neuromuscular index) were calculated. Food restriction altered skull size and shape. Size changes were due to arrested lengths in all studied skull bones. Shape variation was evident by orthocephalization changes, reflected in angulation changes of bones belonging to the frontoethmofacial (frontal, nasal, and maxillary bones) and to the occipitointerparietal (interparietal bone) complexes. Partial restorations by both protein or carbohydrate supplementation were found. Nutritional stresses during lactation affected orthocephalization through an altered growth ratio between two soft tissues functionally associated to the craniofacial complex: brain and masticatory muscles.