Improving grain yield under drought stress is an important breeding objective in rainfed rice-based cropping systems. Much research indicates that yield under drought stress, like yield under optimal conditions, is a polygenic trait with moderate broad-sense heritability in rice. Yield under drought stress is a function of both yield potential under non-stress conditions and genetic factors that are discernible only under stress. A series of experiments indicated that, in some rice populations, one or a few large-effect QTLs acting additively control a substantial proportion of the genetic variation in yield under stress. One such QTL, on chromosome 12, has been shown to account for approximately 50% of the genetic variation in yield under upland stress, in recombinant inbred lines (RIL) derived from the population Vandana/Way Rarem in the combined analysis over 2 years. In another RIL population derived from the lowland rice cross IRCT9993/IR62266, a single QTL located on chromosome 1 accounted for over 30% of genetic variation for yield under stress over 2 years, which was nearly all of the variation not accounted for by variation in yield potential. In a third population, derived from the cross Apo/Swarna² and evaluated in a single dry season under mild aerobic stress, a single QTL on chromosome 6, near RM520, explained over 50% of the genetic variance for yield under aerobic conditions. These loci account for much of the variation in yield under stress that is not explained by variation in yield potential, and have effects that are large enough to permit their detection via bulk segregant analysis.