The study assessed the differences in electromyographic (EMG) activity recorded during clenching in women with chronic unilateral temporomandibular disorders (TMDs) as compared to control subjects. Seventy-five full dentate, normo-occlusion, right-handed, similarly aged female subjects were recruited. Twenty five subjects presented with right side TMD, 25 presented with left side TMD and 25 pain-free control subjects participated. Using integrated surface EMG over a 1 s contraction, the anterior temporalis and masseter muscles were evaluated bilaterally while subjects performed maximum voluntary clenching. Lower EMG activation was observed in patients with TMD as compared to control subjects (temporalis: 195.74+/-18.57 vs. 275.74+/-22.11, P=0.011; masseters: 151.09+/-17.37 vs. 283.29+/-31.87, P<0.001). An asymmetry index (SAI) was calculated to determine ratios of right to left sided activation. Patients with right-sided TMD demonstrated preferential use of their left-sided muscles (SAI -5.35+/-4.02) whereas patients with left-sided TMD demonstrated preferential use of their right-sided muscles (SAI 6.95+/-2.82), (P=0.016). This unilateral reduction in temporalis and masseter activity could be considered as a specific protective functional adaptation of the neuromuscular system due to nociceptive input. The asymmetry index (SAI) may be a useful measure in discriminating patients with right vs. left-sided TMD.