Stored ‘Jonathan’ apple (Malus domestica Borkh) fruit from poorly aerated trickle-irrigated plots had a high incidence of “Jonathan breakdown” (starting as flesh browning beneath the peel) and, from sprinkle-irrigated plots, “Senescent breakdown” (starting from the core area). The flesh of such fruit was high in ethanol at picking time and in acetaldehyde after several months of storage. High ethanol levels in the fruit after 4 months of storage were related to a high ethylene production of the fruit. High soluble solid levels were characteristic of fruit prone to Jonathan breakdown but not to senescent breakdown. The acid content of the fruit flesh was directly correlated with the acetaldehyde content after several months of storage. The acetaldehyde content of the flesh of fruit from plots suffering from root hypoxia rose after 3 months of storage at 1°C. In contrast, the ethanol content of healthy fruit decreased gradually during storage. Fruit from plots suffering from root hypoxia, and particularly their peel, were low in Ca, Β, and Fe, but high in K. Low fruit Ca was related to high acid, acetaldehyde, and sorbitol levels. Fruit low in Ca softened rapidly in storage.