Consumption of fresh apple fruits can induce allergic reactions in humans. The apple allergen Mal d 1 is responsible for these allergic reactions in humans in Central Europe and North America. Biosynthesis of Mal d 1 depends on apple cultivar, and its concentration increases with time during fruit storage. However, data on the impact of different fruit storage conditions during long-term storage are scarce. Hence, the Mal d 1 contents of eight apple cultivars were analyzed for this study during long-term storage in a cold chamber as well as under controlled atmosphere conditions (CA). After harvest, apple fruits were stored for 12, 20, 28 or 36 weeks in a cold-chamber at + 2 °C or as under controlled atmosphere conditions of 1.5 % CO2, 1.5 % O2 at + 2 °C. Mal d 1 content in apple fruit of all eight cultivars examined increased during fruit storage. In most cases, differences between Mal d 1 of apple fruits stored in the cold chamber and under CA conditions were significant, but inconsistent. In apple cv. 'Elise', fruits stored in the cold chamber contained more Mal d 1 compared with those stored in CA, whereas the situation reversed in other varieties like cv. 'Boskoop'. The greatest Mal d 1 content was measured in fruits of cvs. 'Golden Delicious' and 'Gala', whereas the smallest Mal d 1 level was in cvs. 'Elise' and 'Pinova' over the whole storage time. Overall, this experiment showed the complexity of the relationship between the Mal d 1 content, allergenicity of apple fruits, different cultivars, storage conditions and storage time. Persons allergic to apple fruits should consume the fruits as fresh as possible or only after a limited storage time. Furthermore, they should prefer apple varieties with a low content of allergenic proteins, such as cv. 'Elise' or cv. 'Boskoop' as a cultivar known for its large polyphenol content. © 2012 Springer-Verlag Berlin Heidelberg.