BACKGROUND: Cranio-cervico-mandibular (CCM) malalignment is associated with forward head posture (FHP) and temporomandibular joint (TMJ) disorders and affects masticatory muscles. OBJECTIVE: This randomized, double-blind controlled trial aimed to compare the efficacy of scapula-thoracic (ST) exercises on temporomandibular and cervical joint position sense and postural stability in individuals with CCM malalignment. METHODS: Fourty-nine participants with CCM malalignment were randomly assigned to the ST exercise group (STEG, n= 24) or the control group (CG, n= 25). STEG included progressive strengthening, proprioceptive, and stabilization exercises. All participants were assessed before treatment, at the end of the 8th week treatment period and at the 12th week post-treatment follow-up. Cranio-vertebral angle measurement, Fonseca’s Questionnaire, Helkimo Clinical Dysfunction Index, TMJ position test, cervical joint position error test and postural stability assessment were used. RESULTS: The TMJ and cervical joint position sense, total sway degree, area gap percentage, sway velocity and antero-posterior body sway results showed significant improvement in the STEG compared to the CG (p< 0.05), however medio-lateral body sway did not differ between groups (p> 0.05). CONCLUSIONS: Postural stability, TMJ and cervical joint position sense appear to be affected in individuals with CCM malalignment. Our results showed that an exercise program including ST stabilization, proprioception and strengthening of the scapular muscles may be effective in the management of CCM malalignment and will allow clinicians to plan holistic treatment.