Background The prevalence of self-reported upper respiratory tract (URT) symptoms in athletes has been traditionally associated with opportunistic infection during the temporal suppression of immune function following prolonged exercise. There is little evidence for this and a competing non-infectious hypothesis has been proposed, whereby the exercise-induced immune system modulations favor the development of atopy and allergic disease, which manifests as URT symptoms. The aim of this study was to examine the association between allergy and URT symptoms in runners following an endurance running event. Methods 208 runners from the 2010 London marathon completed the validated Allergy Questionnaire for Athletes (AQUA) and had serum analysed for total and specific IgE to common inhalant allergens. Participants who completed the marathon and non-running controls, who lived in the same household, were asked to complete a diary on URT symptoms. Results 40% of runners had allergy as defined by both a positive AQUA and elevated specific IgE. 47% of runners suffered from URT symptoms following the marathon. A positive AQUA was a significant predictor of post-marathon URT symptoms in runners. Only 19% of nonrunning controls reported symptoms. Conclusions Prevalence of allergy in recreational marathon runners was similar to that in elite athletes and higher than the general population. There was a strong association between a positive AQUA and URT symptoms. The low proportion of households in which both runners and non-runners were symptomatic suggests that the nature of symptoms may be allergic or inflammatory based rather than infectious. Allergy is a treatable condition and its potential impact on performance and health may be avoided by accurate clinical diagnosis and management. Both athletes' and coaches awareness of the potential implications of poorly managed allergy needs to be raised.