When defining allergic outcomes in epidemiology studies, results of the skin prick test (SPT) panel are often dichotomized as positive/negative or categorized based on the number of positive responses. Item response theory (IRT) models, however, may prove to be a better alternative with the ability to generate scores that account for both type and number of positive SPTs. IRT was applied to SPT responses administered to 537 children at age two to determine predictability of allergic disease at age four. The children received SPTs to 15 aeroallergens and two foods. Atopy predisposition scores were obtained from the IRT model using the posterior distribution of the latent trait, atopy. These scores were used to predict persistent wheeze, rhino-conjunctivitis, and eczema at age four. Results were compared to the dichotomized and categorical (positive to ≥2, positive to one, vs. negative to all allergens) SPT variables. At age two, 39% of children had at least one positive SPT. All three allergic disease outcomes were significantly associated with IRT atopy scores: persistent wheeze odds ratio (OR) = 1.7 (95% confidence interval (CI): 1.2, 2.3); rhino-conjunctivitis OR = 1.7 (95% CI: 1.2, 2.3); eczema OR = 1.6 (95% CI: 1.2, 2.3). In contrast, rhino-conjunctivitis was the only outcome significantly associated with the dichotomized SPT variable with an OR = 1.9 (95% CI: 1.2, 3.0). For the categorical SPT variable, all three allergic symptoms were significantly associated with positive to ≥2 allergens compared to negative to all, but no difference was observed between those with positive to one compared to negative to all. The IRT model proved to be an informative methodology to assess the predictability of early SPT responses and identify the allergens most associated with atopy predisposition.