OBJECTIVE: To investigate autonomic abnormalities in male and female fibromyalgia (FM) and Gulf War illness (GWI) patients by comparing heart rate variability (HRV) with that of age- and sex-matched healthy controls. METHODS: Subjects included 26 (19 women, 7 men) with FM, 11 (6 men, 5 women) with GWI, and 36 (18 men,18 women) healthy controls. HRV was determined from Holter recordings obtained in the Clinical Research Center. Analysis of variance compared 24-hour, daytime, and nighttime HRV by sex within groups and by group within sex. RESULTS: In women with FM or GWI, HRV was significantly lower than in men with FM or GWI. HRV was similar in male and female controls. When HRV was compared by group within sex, HRV was significantly decreased in women with FM or GWI and no significant differences were seen for men with these conditions. CONCLUSION: Decreased HRV in FM and GWI appears to be sex dependent. Results suggest that different mechanisms may be operative in symptom expression in men and women with this spectrum of illness.