Fibromyalgia syndrome (FMS) is characterized by systemic pain of unknown etiology, and is often accompanied by various psychological symptoms. In the present study, differences in surface electromyographic (SEMG) levels of the trapezius muscle, skin temperature (TEMP) and skin conductance level (SCL) were compared between the right and left side of the body in 31 FMS and 47 control subjects (Control Group). We observed significant asymmetries of SEMG level, TEMP and SCL in the FMS Group. These asymmetries might be related to central, peripheral and autonomic nervous system dysfunctions. Marked increase of SEMG levels, and a decrease of TEMP and SCL were observed at the dominant side in the FMS Group, and a negative correlation of SEMG levels with TEMP and SCL was found. These results suggest that continued antalgic postures in response to pain at the dominant side in FMS patients might lead to asymmetries of SEMG level, TEMP and SCL. Thus, a focus on pain related behaviors and muscle asymmetry might be a useful therapeutic approach.