The study was designed to investigate the autonomic dysfunction in fibromyalgia syndrome (FMS) by recording sympathetic skin response (SSR) from palmar, plantar and genital regions. The second aim was to evaluate the relation between sexual problems and autonomic dysfunction in FMS. SSR potential was recorded from palmar, plantar and genital regions in 28 married, female FMS patients and 18 married, healthy females. Fibromyalgia Impact Questionnaire (FIQ) was used to show the clinical severity and functional disability in FMS patients. Glombok Rust Inventory of Sexual Satisfaction (GRISS), a 28-item questionnaire, was used to assess the existence and severity of sexual problems. Beck test was used to evaluate anxiety and depression. The amplitude of SSR recorded from palmar, plantar and genital regions was lower than in the control subjects (P < 0.05). GRISS (total and subscale), Beck test and FIQ scores of FMS patients were higher than in the control subjects (P < 0.05). No correlation was found between the SSR potential and GRISS scores. The results of our study reveal that abnormality in SSR recorded from palmar, plantar and genital regions reflects the abnormality in the autonomic nervous system (ANS) of FMS patients. These patients have more sexual problems than healthy subjects, and we think this finding is related to increased anxiety and depression in these patients.