Temporomandibular disorders are the most common condition affecting the orofacial region, resulting in pain and dysfunction. This study aimed to elucidate the ambiguous association between cervical features and temporomandibular disorders by measuring the rotations between the skull-atlas, atlas-axis and mandible-atlas and examining the relationship between these rotations and temporomandibular disorders. Cone-beam computed tomography (CBCT) images from 176 patients, 97 females and 79 males with an average age of 25.7 years were used in this study. The patients were divided into two groups: those with joint dysfunction (n = 88) and those without (n = 88). The study employed various methods to determine rotations in the skull-atlas, atlas-axis and mandible atlas based on anatomical landmarks and measurements. These methods include the use of specific planes, angles and distances to identify and measure rotation. Data analysis was performed using the TURCOSA statistical software (Turcosa Analytics Ltd Co, Turkey, www.turcosa.com.tr). The results showed that the degree of rotation between the skull and the atlas was higher in the TMD group than in the control group (p < .001). Similarly, Atlas-axis rotation was significantly higher in the TMD group (p < .001). However, no significant difference was found between mandible atlas rotations in the two groups (p = .546). The study also found a significant difference between the direction of rotation between the atlas and axis and the direction of mandible atlas rotation (p < .001) as well as between skull and atlas rotations and mandible-atlas rotations (p < .001). Overall, the study suggests that there is a relationship between the skeletal structures of the cranio-cervico-mandibular system and TMD. Skull-atlas and atlas-axis rotations may play an important role in the aetiology of TMD in individuals with TMD. Therefore, it is important to evaluate rotations in the skull-atlas-axis region for the treatment of TMD.