Upper respiratory tract infections (URIs) are a common complaint in competitive swimmers and can adversely affect performance. No intervention has yet been shown to reduce URI incidence in intensively trained athletes. The University of Virginia varsity swim team received three weeks of training in qigong for the purpose of reducing stress and improving health. Our primary objective was to assess the relationship between qigong practice and symptoms of URI during a time when swimmers would be at high URI risk. Secondary objectives were to assess degree of compliance with a qigong practice regimen, to evaluate differences between qigong practitioners and non-practitioners, and to determine the response-rate and reliability of a newly developed internet-based, self-report survey. The design was observational, cross-sectional, and prospective. Weekly data on cold and flu symptoms, concurrent health problems and medication use, and qigong practice were gathered for seven weeks. Retrospective information on health and qigong training response was also collected. Participants were 27 of the 55 members of the University of Virginia Swim Team in the Virginia Athletic Department. Main outcomes were measures of aggregated cold/flu symptoms and Qigong practice. Survey completion was 100%, with no missing data, and reliability of the instrument was acceptable. Cold and flu symptoms showed a significant non-linear association with frequency of qigong practice (R(2) = 0.33, p < 0.01), with a strong, inverse relationship between practice frequency and symptom scores in swimmers who practised qigong at least once per week (R(2) = 0.70, p < 0.01). Qigong practitioners did not differ from non-practitioners in demographic or lifestyle characteristics, medical history, supplement or medication use, or belief in qigong. These preliminary findings suggest that qigong practice may be protective against URIs among elite swimmers who practice at least once per week.