Apple is one of the most worldwide-consumed fruits and a number of cultivars, differing in organoleptic and nutritional characteristics, are available for the market. Annurca apple is a regional variety from Southern Italy, which is known for crispness, excellent taste and long shelf life of fruits. These features have renewed the interest in the investigation of their genetic potential and different studies have lead to their partial genetic and metabolic characterisation. In this study, we present the analysis of the protein repertoire of the pseudocarp tissues of three accessions of Malus x domestica Borkh. cv. Annurca, as first example of the systematic annotation of the apple proteome. Proteins were extracted from fruit tissues and resolved on 2-DE gels; commonly expressed proteins were in-gel digested and analysed by MALDI-TOF-MS and μLC-ESI-IT-MS/MS approaches. Peptide MS and MS/MS data were searched against publicly available protein and EST databases, and 44 spots were identified and associated to 28 different species. They were related to important physiological processes such as energy production, ripening and stress response. The occurrence of allergens causative of widespread food allergy syndromes was also detected. Integration of genomic, metabolomic and proteomic data will be indispensable for future molecular characterisation and hence full exploitation of the peculiar organoleptic, nutritional and agronomic traits of local cultivars of fruits.