This study was conducted in order to determine the effects of body position on electromyographic (EMG) activity of sternocleidomastoid and masseter muscles, in 15 patients with myogenic cranio-cervical-mandibular dysfunction undergoing occlusal splint therapy. EMG activity was recorded by placing surface electrodes on the sternocleidomastoid and masseter muscles (contralateral to the habitual sleeping side of each patient). EMG activity at rest and during swallowing of saliva and maximal voluntary clenching was recorded in the following body positions: standing, supine and lateral decubitus. In the sternocleidomastoid muscle significant higher EMG activities at rest and during swallowing were recorded in the lateral decubitus position, whereas during maximal voluntary clenching EMG activity did not change. In the masseter muscle significant higher EMG activity during maximal voluntary clenching in a standing position was observed, whereas EMG activity at rest and during swallowing did not change. The opposite pattern of EMG activity supports the idea that there may exist a differential modulation of the motor neuron pools of the sternocleidomastoid and masseter muscles, of peripheral and/or central origin. This suggests that the presence of parafunctional habits and body position could be closely correlated with the clinical symptomatology in these muscles in patients with myogenic craniomandibular dysfunction.