Simple SummaryPhenotypic variability can be structured according to three interrelated components: developmental stability, morphological integration, and canalization. The cranium presents modular organization, consistent with the principles of morphological integration. In Down syndrome (DS), the most common genetic aneuploidy, the integration of the cranial-vertebral-maxillary complex, remains unknown. This study aimed to analyze whether there are significant relationships between the skull base, atlantoaxial joint, and maxillary-mandibular complex in a study group of 41 individuals with DS and nonsyndromic controls. Twenty-nine measurements were performed on each participant’s cone-beam computed tomography images, which were grouped into three blocks: atlantoaxial dimensions, craniovertebral dimensions, and cephalometric dimensions. With regard to the association between blocks, we found no significant relationship in the DS group. However, we confirmed a statistically significant correlation between all blocks of variables in the controls. In conclusion, these results confirm a very poor morphological integration of the cranial-cervical-maxillary complex in individuals with DS. This finding reinforces the proposal that gene overload enhances canalization, which could potentially affect the outcomes of certain orthopedic and surgical procedures.Background: Morphological integration refers to the tendency of anatomical structures to show correlated variations because they develop in response to shared developmental processes or function in concert with other structures. The objective of this study was to determine the relationships between the dimensions of different cranial-cervical-facial structures in patients with Down syndrome (DS). Methodology: The study group consisted of 41 individuals with DS who had undergone cone-beam computed tomography (CBCT) at the Dental Radiology Unit of the University of Santiago de Compostela (Spain). In the historical archive of this same unit, 41 CBCTs belonging to individuals with no known systemic disorders or severe malformations of the maxillofacial region were selected, forming an age and sex-matched control group. Twenty-nine measurements were performed on each participant’s CBCT images, which were grouped into three blocks: atlantoaxial dimensions, craniovertebral dimensions and cephalometric dimensions. To determine whether there were significant differences between the dimensions obtained in the DS and control groups, we applied multiple analysis of variance and linear discriminant analysis tests. The analysis of the association between blocks (in pairs) was performed with the canonical correlation analysis test. Results: The dimensions evaluated in the three blocks of variables of individuals with DS differ significantly from those of nonsyndromic controls (p < 0.001). The highest discriminative capacity to identify controls and patients with DS was obtained with the cephalometric dimensions (87.5%). With regard to the association between blocks (two-by-two measurements), we found no significant relationship in the DS group. However, we confirmed a statistically significant correlation between all pairs of blocks of variables in the controls, especially between the atlantoaxial and cephalometric dimensions (p < 0.001) and between the craniovertebral and cephalometric dimensions (p < 0.001). Conclusions: Our results confirm a very poor morphological integration of the cranial-cervical-maxillary complex in individuals with DS. This finding reinforces the proposal that gene overload enhances the channeling process.