Growth of different body parts in humans is sensitive to different resource constraints that are mediated by parental investment. Parental investment can involve the expenditure of material, cognitive, and emotional resources on offspring. Cranial volume, an important predictor of cognitive ability, appears understudied in this context. We asked (1) whether there are associations between growth and family structure, self-reported estimates for resource availability, and sibling number; and (2) whether these constraints relate to head and body growth in a similar manner. We assessed the associations between parental investment, height, and cranial volume in a cross-sectional study of Estonian children (born 1980–87, aged 11–17). Height correlated negatively with the number of siblings but this association became negligible in a model controlling for birthweight, parental heights, and mother’s age at birth. Unlike height, cranial volume was unrelated to sibling number, but it was negatively associated with self-reported meat and general resource shortage. Cranial volume was related to family structure and paternal education. Children living with both birth-parents had larger heads than those living in families containing a step-parent. Since these family types did not differ with respect to meat or general resource shortage, our findings suggest that families including both genetic parents provide non-material benefits that stimulate predominantly cranial growth. For the studied developmental period, cranial volume appeared a more sensitive marker of growth constraints than height. The potential of using cranial volume for quantifying physical impact of non-material parental investment deserves further attention.