BACKGROUND Atopy and allergic rhinitis are thought to be increased in prevalence in chronic fatigue syndrome (CFS). METHODS To investigate this hypothesis, 51 CFS (CFS), 34 normal (N), 27 allergic rhinitis (AR), and 17 patients with other rheumatologic diseases filled out an Airway Symptom Severity self-report questionnaire to determine the frequencies of nasal, sinus, and chest symptoms, and a Systemic Complaints self-report questionnaire to determine the frequencies of complaints referable to neurologic, rheumatologic, gastrointestinal, and other systems. All subjects received a standard set of allergy skin tests, and were subdivided into those with positive and negative results. RESULTS Allergy skin tests were positive in 35% of CFS and 44% of N subjects (difference not significant by Chi2). Significant rhinitis complaints were present in 83% of skin test positive CFS, 76% of skin test negative CFS, 74% of AR, and 23% of N subjects. Systemic Complaints scores were significantly elevated in skin test positive (94%) and negative (94%) CFS groups compared with AR (35%) and N (6%) groups. This score could significantly discriminate between CFS and N subjects. CONCLUSIONS These data indicate that in this CFS population, 24% had no significant rhinitis complaints, 30% had positive skin tests suggesting the potential for allergic rhinitis complaints, and 46% had nonallergic rhinitis. The mechanism of the nonallergic component may offer insights into the pathogenesis of CFS.