BACKGROUND Type I allergy and allergic asthma are common diseases in the developed world associated with IgE antibodies and Th2 cell reactivity. To date, the only causative treatment for allergic disease is specific immunotherapy (SIT). METHOD Here, we review recent works from our laboratory focused on identifying human T cell epitopes associated with allergic disease and their potential use as biomarkers or therapeutic targets for SIT. In previous studies, we have mapped T cell epitopes associated with the major 10 timothy grass (Tg) allergens, defined on the basis of human IgE reactivity by ELISPOT. RESULTS Interestingly, in about 33% of allergic donors, no T cell epitopes from overlapping peptides spanning the entire sequences of these allergens were identified despite vigorous T cell responses to the Tg extract. Using a bioinformatic-proteomic approach, we identified a set of 93 novel Tg proteins, many of which were found to elicit IL-5 production in T cells from allergic donors despite lacking IgE reactivity. Next, we assessed T cell responses to the novel Tg proteins in donors who had been treated with subcutaneous SIT. A subset of these proteins showed a strong reduction of IL-5 responses in donors who had received subcutaneous SIT compared to allergic donors, which correlated with patients' self-reported improvement of allergic symptoms. CONCLUSION A bioinformatic-proteomic approach has successfully identified additional Tg-derived T cell targets independent of IgE reactivity. This method can be applied to other allergies potentially leading to the discovery of promising therapeutic targets for allergen-specific immunotherapy.