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To characterize the etiology of upper respiratory symptoms in elite athletes presenting to a sports physician for treatment.Prospective clinical and laboratory investigations.Sports medicine clinic.Seventy elite-level athletes.Physician-recorded symptoms and diagnosis; health/training questionnaires; laboratory investigations of respiratory pathogens, white blood cell differential counts, and immune parameters.Physicians characterized 89% of presentations as viral or bacterial upper respiratory tract infection. Only 57% of presentations were associated with an identified pathogen or other laboratory parameters indicative of infection. Demographic information, previous illness, and training history did not distinguish between presentations with or without objective measures of infection. Elevated white blood cell and neutrophil counts and lower vitamin D concentrations partially distinguished infectious episodes. The number of systemic symptoms/behaviors at presentation (cough, headache, earache, fatigue, fever/rigors, myalgia/arthralgia, or cessation of training before clinic attendance) had some predictive value for infection: odds ratio per symptom, 1.23 (90% confidence interval: 0.91 to 1.66); probability of infection, 48% with no symptoms to 77% with 6 symptoms. Laboratory investigation identified allergy in a considerable proportion of the cohort (39%).The discrepancy between physician and laboratory diagnosed infection in elite athletes highlights the need for consideration of alternate diagnostic options when evaluating upper respiratory symptoms in athletes. A considerable proportion of episodes of respiratory symptoms in athletes were not associated with identification of a respiratory pathogen; other potentially treatable causes of upper respiratory symptoms should be considered, particularly in athletes with recurrent symptoms.