Geohelminth infections may affect the expression of allergic disease. To investigate the relationship between geohelminth infections, atopy, and symptoms of allergic disease, we studied 4,433 schoolchildren from 71 schools in a rural tropical area in Ecuador. Information was collected on allergic symptoms, allergen skin test reactivity, and presence of geohelminth infections. Allergic symptoms were of low prevalence (2.1% had recent wheeze), but prevalence of skin test reactivity was relatively high (18.2%). The presence of geohelminth infections was protective against allergen skin test reactivity (odds ratio 0.62, 95% confidence interval 0.50–0.76, p < 0.001) and symptoms of exercise-induced wheeze (odds ratio 0.59, 95% confidence interval 0.40–0.87, p = 0.008) but not against other wheeze symptoms or symptoms of allergic rhinitis or atopic eczema. Infection intensity with Ascaris lumbricoides or Trichuris trichiura was associated with a reduction in the prevalence of allergen skin test reactivity but not with allergic symptoms. There was no evidence of interactions between geohelminth infection and allergen skin test reactivity on the risks of allergic symptoms. The results suggest that geohelminth infections do not explain the low prevalence of allergic symptoms in the study population.