Rootstock significantly affected the development of stem-end rind breakdown (SERB) on `Valencia' and navel oranges (Citrus sinensis), but not `Ray Ruby' grapefruit (C. paradisi) or `Oroblanco' (C. grandis × C. paradisi), and affected postharvest decay on navel orange, `Ray Ruby' grapefruit, `Oroblanco' and one of two seasons (2002) on `Valencia' orange. In `Valencia' and navel oranges, fruit from trees grown on Gou Tou (unidentified Citrus hybrid) consistently developed low SERB. `Valencia' oranges on US-952 [(C. paradisi × C. reticulata) × Poncirus trifoliata] developed high levels of SERB in both years tested. Relative SERB of fruit from other rootstocks was more variable. Navel oranges, `Ray Ruby' grapefruit, and `Oroblanco' fruit from trees on Cleopatra mandarin (C. reticulata) rootstock consistently developed relatively low levels of decay, and in navel this level was significantly lower than observed from trees on all other rootstocks. In three of five trials we observed significant differences between widely used commercial rootstocks in their effects on postharvest SERB and/or decay. Given the expanding importance of sales to distant markets, it is suggested that evaluations of quality retention during storage be included when developing citrus rootstocks and scion varieties for the fresh market.