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Introduction Different types of headaches and TMJ click influence the masseter muscle activity. The aim of this study was to assess the trend of energy level of the electromyography (EMG) activity of the masseter muscle during open-close clench cycles in migraine without aura (MOA) and tension-type headache (TTH) with or without TMJ click. Methods Twenty-five women with MOA and twenty four women with TTH participated in the study. They matched with 25 healthy subjects, in terms of class of occlusion and prevalence of temporomandibular joint (TMJ) with click. The EMG of both masseter muscles were recorded during open-close clench cycles at a rate of 80 cycles per minute for 15 seconds. The mouth opening was restricted to two centimeters by mandibular motion frame. Signal processing steps have been done on the EMG as: noise removing, smoothing, feature extraction, and statistical analyzing. The six statistical parameters of energy computed were mean, Variance, Skewness, Kurtosis, and first and second half energy over all signal energy. Results A three-way ANOVA indicated that during all the cycles, the mean of energy was more and there was a delay in showing the peak of energy in the masseter of the left side with clicked TMJ in MOA group compared to the two other groups, while this pattern occurred inversely in the side with no-clicked TMJ (P |