Most of the allergenic proteins from fruits identified so far belong to different families of pathogenesis-related (PR) proteins. These PR proteins have been classified in different families of structurally and functionally unrelated proteins, but the majority of all fruit allergens belong to three groups, in particular PR-5 thaumatin-like proteins (TLP), PR-10 Bet v 1-like proteins, and PR-14 non-specific lipid transfer proteins (nsTLP). Some allergenic proteins from fruits can also be found among PR-protein families of PR-2 β1,3-glucanase proteins, PR-3 chitinases I, II, IV–VII, and PR-8 chitinases III. In addition, other important fruit allergens occur in protein families unrelated to the PR-protein families, such as the profilins and the newly emerging group of gibberellin-regulated proteins (GBRP). Finally, proteins that belong to seed storage proteins from higher plants, including 2S albumins, 7S globulins (vicilin), and 11S globulins (legumin), must be retained as possible potential fruit allergens resulting from the unintended consumption of the seeds. Here, we present an overview of the structural organization, functional properties, and phylogenetical relationships among these different groups of fruit allergens, supporting the occurrence of cross-reactivity and cross-allergenicity often described between fruit allergens, and the corresponding allergens from vegetables and pollens.