Trivalent aluminium (Al3+) is the major toxin encountered by plants on acid soils. These cations inhibit root growth by damaging cells at the root apex. The physiology and genetics of Al3+ tolerance mechanisms involving organic anion efflux from roots have now been investigated in a range of species. Over the past decade, genes encoding these and other newly discovered mechanisms of tolerance have been cloned. In this review, we describe the genes controlling the genotypic variation in Al3+ tolerance for several important crop species. We focus on recent insights into the transcriptional regulation of these and other genes involved in Al3+ tolerance and discuss the pathways coordinating their expression in Arabidopsis and rice.