INTRODUCTION Head and neck skeletal anomalies or normal variants might predict the occurrence of palatally displaced impacted maxillary canines. Despite their clinical importance, studies in this regard are rare, especially when it comes to vertebral anomalies. METHODS This case-control study was performed on cephalographs of 35 orthodontic patients (11 male, 24 female) with palatally displaced canines (PDC) and 75 patients without them (29 male, 46 female). PDC were diagnosed on panoramic and lateral cephalographs and from clinical reports. The occurrence and severity of sella turcica bridge and the atlas ponticulus posticus, and deficiency of the posterior atlas arch were evaluated twice on lateral cephalographs. The associations between the occurrence and level of these skeletal anomalies and variations of PDC occurrence as well as additional correlations were assessed using multivariable and bivariate statistics (α = 0.05; β ≤0.2). RESULTS The patients' mean age was 18.4 ± 1.9 years. In the control and patient groups, 23 (30.7%) and 21 subjects (60%) had sella turcica bridging, respectively (chi-square, P = 0.003). Ponticulus posticus was observed in 14 (18.7%) controls and 15 (42.9%) patients (chi-square, P = 0.007). Posterior atlas arch deficiency was observed in 4 (5.3%) controls and 5 (14.3%) patients (chi-square, P = 0.111). The presence of ponticulus posticus and sella turcica bridging might be associated with increased odds of PDC occurrence for about odds ratios of 3.1 and 3.5 times, respectively (binary logistic regression). CONCLUSIONS PDC is positively associated with the occurrence and severity of sella turcica bridging and ponticulus posticus. The association between PDC and posterior atlas arch deficiency was inconclusive.