This study aimed to investigate the immunomodulatory and antiallergic properties of preparations from lemon, Citrus medica L. (citrus), and quince, Cydonia oblonga Mill. (Cydonia), which are used in pharmaceutical products to treat patients suffering from allergic disorders. Preparations were analyzed with respect to their impact on the degranulation capacity from basophilic cells as well as mediator release from activated human mast cells in vitro, including IL-8 and TNF- α secretion. The results show that the degranulation of basophilic cells was diminished only in the presence of Citrus, and this effect was compared to the synthetic drug azelastine. Furthermore, Citrus and Cydonia both inhibited the production of IL-8 and TNF- α from human mast cells, and at low concentrations additive effects were observed. As a positive inhibition control, dexamethasone was used. LC-MS analyses showed that the major phenolic components in extracts from Citrus and Cydonia are eriocitrin and neochlorogenic acid, respectively. Nevertheless, these compounds do not show biological effects at concentration levels detected in their corresponding extracts. In conclusion, the present data provide a rational base for the use of the single pharmaceutical preparations from Citrus and Cydonia in a differentiated treatment of allergic disorders in part by the regulation of soluble allergic mediators from basophilic cells and mast cells.