Water deficits and high temperature are major abiotic stresses affecting crop productivity. In order to unravel the genetic architecture of maize tolerance to these stresses, linkage analysis between the expression of the two tolerance traits and allelic composition of molecular markers was performed. The study was carried out on two separate panels of recombinant inbred lines (RILs). The first, T Γ CM, consists of 48 RILs for which a densely saturated molecular marker map was already available and was used for thermotolerance analysis; the second panel, B73 Γ H99, 142 RILs, was characterized by 50 RFLPs and 70 microsatellites and was used for water stress tolerance evaluation. Different components for the two tolerance traits were analyzed, and for each of them several quantitative trait loci (QTLs) were detected. With the aim of identifying "major QTLs," potential candidates for marker-assisted selection, the map positions of the QTLs detected for the different components and in the two panels were compared. The analysis revealed four genomic regions, on chromosomes 2, 4, and 6, containing factors controlling cell membrane stability, a major tolerance component, under both high temperature and water stress. Furthermore, a preliminary analysis indicated that some rab genes, known to be induced by drought and abscissic acid, roughly map to the same regions as QTLs for water stress tolerance. These data are discussed in relation to a possible role of these genes in providing tolerance to water deficits.