Iron toxicity is a major constraint to rice production, particularly in highly-weathered soils of inland valleys in sub-Saharan Africa where the rice area is rapidly expanding. Although there is wide variation in tolerance in the rice germplasm, progress in introgressing tolerance traits into high-yielding germplasm has been slow owing to the complexity of tolerance mechanisms and large genotype by environment effects. We review current understanding of tolerance mechanisms, particularly those involving below-ground plant-soil interactions, which to date have been less studied than above-ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below-ground processes controlling Fe retention in roots and root-shoot transport, and also plant Fe sensing. We conclude that future breeding programs should be based on well-characterised molecular markers for tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods developed for individual mechanisms.