BACKGROUND: Unexplained chronic fatigue is a frequent complaint in primary care. A prospective observational study design was used to evaluate whether certain commonly used therapies for unexplained chronic fatigue may be effective. METHOD: Subjects with unexplained chronic fatigue of unknown etiology for at least 6 months were recruited from the Wisconsin Chronic Fatigue Syndrome Association, primary care clinics, and community chronic fatigue syndrome presentations. The primary outcome measure was change in a 5-question fatigue score from 6 months to 2 years. Self-reported interventions tested included prescribed medications, non-prescribed supplements and herbs, lifestyle changes, alternative therapies, and psychological support. Linear regression analysis was used to test the association of each therapy with the outcome measure after adjusting for statistically significant prognostic factors. RESULTS: 155 subjects provided information on fatigue and treatments at baseline and follow-up. Of these subjects, 87% were female and 79% were middle-aged. The median duration of fatigue was 6.7 years. The percentage of users who found a treatment helpful was greatest for coenzyme Q10 (69% of 13 subjects), dehydroepiandrosterone (DHEA) (65% of 17 subjects), and ginseng (56% of 18 subjects). Treatments at 6 months that predicted subsequent fatigue improvement were vitamins (p = .08), vigorous exercise (p = .09), and yoga (p = .002). Magnesium (p = .002) and support groups (p = .06) were strongly associated with fatigue worsening from 6 months to 2 years. Yoga appeared to be most effective for subjects who did not have unclear thinking associated with the fatigue. CONCLUSION: Certain alternative therapies for unexplained chronic fatigue, especially yoga, deserve testing in randomized controlled trials.