The craniofacial morphology of Class III children with a full deciduous dentition was investigated by means of a cephalometric and correlation study. A group of 69 Class III subjects was compared to a group of 60 Class I subjects during the phase of the primary dentition. Each group was then divided into three age subgroups (4, 5, and 6 years) and a comparison was also performed between Class III and Class I subgroups. According to the results, early signs of Class III skeletal disharmony are present during the deciduous dentition phase. A larger mandibular body length (P < 0.001), a greater value for the ratio between the extent of the anterior cranial base and the mandibular body length (P < 0.001), and a forward positioning of the mandible (< P0.01 < 0.001) were consistently found in Class III children at the ages of 4, 5, and 6 years. A correlation analysis between all the cephalometric measurements in the Class III and Class I groups was then carried out, and the significance of the differences between correlation coefficients of the two groups was calculated. A distinctive Class III pattern of non-topographical associations between anterior cranial base and mandibular measurements could be detected.