The apple fruit (Malus domestica L. Borkh) is one of the most popular fruits worldwide. Beyond their beneficial properties, apples contain proteins that trigger allergic reactions in susceptible consumers. Mal d1 to 4 are allergens present in a variety of different isoforms in apples, with Mal d1 and Mal d3 being the main allergens. In this study, we used proteomics to quantify all four Mal d proteins in 52 apple genotypes with varying allergenic potentials. We revealed the expression of at least 21 Mal d1 isoforms while two Mal d3 and two Mal d4 proteins were found among the genotypes. The allergenic potential of the Mal d isoforms was characterized by comparing isoform abundance with allergenic scores of genotypes (from oral challenge tests). The Mal d peptides detected by comparative analysis presumably have different IgE binding properties and could therefore be used as potential molecular markers to discriminate between hypoallergenic and hyperallergenic cultivars.