Regular consumption of fruits has a positive influence on human health by disease prevention. However parallel to dietetic benefits, IgE-mediated fruit allergies have been shown to be an increasing health risk for children and adults in the Northern hemisphere. The spectrum of food allergies ranges from chronic symptoms to more acute problems and even anaphylaxis. Fruit proteins with high primary sequence similarity display also homologous tertiary structures, resulting in similar epitopes to IgEs and consequently in cross-reactivity. In this review we present the major allergens of stone and pome fruits and discuss the presence of homologous proteins in small fruits. Interestingly these proteins, which might pose an allergenic potential for pre-sensitised individuals are expressed also in strawberry, raspberry and blueberry, otherwise rich in beneficial biofactors.