The largest differences in intraspecific head shape among the Carnivora order are to be found in dogs. Based on their skull morphotypes, dog breeds are currently classified as dolichocephalic, mesaticephalic and brachycephalic. Due to the fact that some breeds have not been yet defined, this classification is incomplete; moreover, multi-breed studies on the skull morphology of puppies have never been performed. The aim of this work was to verify (i) whether differences in the skull conformation of purebred puppies are already present within the first week of age; (ii) whether radiographic and anatomic measures could be considered interchangeable, and (iii) to possibly classify puppies from non-categorized breeds thanks to their radiographic cranial measurements using neural nets. One hundred and thirty-seven dead puppies aged 0-7 days were examined considering their anatomic and radiographic measures. All linear measures and anatomic indices significantly differed among brachycephalic and non-brachycephalic puppies. Radiographic indices, with the exception of CI, identified the three skull morphotypes (p<0.05, for all comparisons). Radiographic and anatomic measures proved to be non-interchangeable in newborn puppies. Finally, nineteen puppies belonging to 5 non-categorized breeds could be classified thanks to neural nets in the three skull morphotypes with different probability (P between 0,66 and 0,95).