Objective: To evaluate the cephalometric characteristics of skulls with and without artificial deformation in a pre-Columbian civilization of the Peruvian Andes (Chavin civilization 900 B.C.To 200 B.C.). Materials and Methods: The study was observational, analytical, retrospective, and comparative in design. The image analysis unit was radiological with cephalometric measurement. The sample consisted of occipito-frontal dry skulls of the Chavín culture (n = 40) with and without artifical deformation, which underwent cephalometric radiography for analysis. Results: The measurements of skull base size, anterior cranial base size, posterior cranial base size, posterior cranial base size, and cranial deflection were greater in the deformed than the non-deformed skulls (95.1 ± 6.6 vs. 92.3 ± 6.2 mm, 61.5 ± 3.6 vs. 61.4 ± 3.6 mm, 39.8 ± 3.4 vs. 38.1 ± 3.5 mm, 136 ± 26.9 vs. 135.0 ± 5.6 mm, and 35.7 ± 31.8 vs. 28.2 ± 14.6 mm, respectively). Significant differences were only found in the posterior cranial base size measurements between deformed and nondeformed skulls (P = 0.008). When comparing the characteristics of the skulls, significant differences were only found between the position of the posterior nasal spine and the maxilla size of the deformed versus the non-deformed skulls (P 0.05). Conclusions: It is concluded that there are differences in the size, position, and inclination of the craniofacial structures between the artificially deformed skulls and the skulls that have not been artificially deformed by the old Chavin civilization.