Alterations in autonomic activity are well established in fibromyalgia syndrome (FMS). Previous studies found reduced parasympathetic activity and sympathetic reactivity to physical and stress manipulations. However, sympathetic activity at rest has not been well studied in FMS. Sweating is exclusively controlled by sympathetic mechanisms. In this study, skin conductance (SC), as an indirect measure of sweating, was analyzed in 45 women with FMS and 38 healthy women. Tonic SC levels were recorded during a 4-minute rest period, and a breathing maneuver consisting of deep breathing with posterior breath holding was used to evoke SC responses. Associations of tonic SC with state anxiety and body temperature, measured in the hand, were explored to determine sweat functionality. The results showed reduced tonic SC levels, with a less marked decrease in SC during the recording period, and blunted SC reactivity to the breathing manipulation in FMS patients relative to healthy participants. Positive associations of SC with state anxiety and body temperature were observed in healthy participants, but these associations were absent in FMS patients. These results indicate alterations of sweating in FMS, suggesting reduced tonic and reactivity sympathetic influences. Furthermore, the absence of associations between SC levels and state anxiety and body temperature in the patient sample suggested a loss of functionality of the autonomic nervous system in FMS. Diminished autonomic regulation in FMS would reduce the ability to cope with environmental demands, thus favoring increases in stress and pain levels. Finally, the observed reduction in sweating is in accordance with evidence of small nerve fiber neuropathy in FMS.