'Haldane's rule', formulated by J. B. S. Haldane in 1922, states that: "When in the F1 offspring of two different animal races one sex is absent, rare, or sterile, that sex is the heterozygous [heterogametic] sex". His rule is now known to apply in mammals, lepidopterans, birds, orthopterans and dipterans. In Drosophila, for example, Bock cites 142 cases of interspecific hybridizations that produce one sterile and one fertile sex in the offspring, all but one of these crosses yielding sterile XY males and fertile XX females. Despite much speculation, however, the genetic basis of Haldane's rule remains unknown. Haldane himself rejected the simple explanation that males are innately more sensitive than females to the effects of hybridization because groups with heterogametic females (such as birds and butterflies) usually show female sterility in hybrids, so that heterogamety itself is the critical feature. He and others suggested that heterogametic infertility or inviability in hybrids arises by a genetic imbalance between X chromosomes and autosomes. An alternative explanation is that this syndrome is caused by a mismatch of X and Y chromosomes. Here I show that in the Drosophila melanogaster subgroup, Haldane's rule for fertility apparently arises from a genetic interaction between X and Y chromosomes and not from an imbalance between sex chromosomes and autosomes. This finding has important implications for understanding the evolution of interspecific reproductive isolation.