Cor a 1, Cor a 8 and Cor a 11 are three important allergens in hazelnut. Aim of this work was to set up a method to quantitatively measure differences in their transcription levels. For the expression study, three different models were set up, taking also into account the ripening stage and the year of harvest. A gene transcription analysis by relative quantification through Real-Time PCR has been developed to measure the transcription profile of hazelnut allergens. Differences in the gene transcription levels of Cor a 8 and Cor a 11 were found, both when comparing different cultivars among themselves and when comparing different years of harvest and ripening stages in the “Tonda Gentile Trilobata” (TGT) cultivar. Major allergen Cor a 1 gene did not display any statistically significant variation in its transcript abundance. Principal Components Analysis (PCA) was finally performed to better elucidate the classification of samples.