The genetic dissection of drought tolerance mechanisms in tropical maize was initiated at the International Maize and Wheat Improvement Center (CIMMYT) about 10 years ago. The initial focus of this approach was to understand the genetic basis, across populations and environments, of drought tolerance at flowering. This involved collecting morphological data and detecting quantitative trait loci (QTLs) for yield components and secondary morphological traits of interest. To provide a suitable biological framework for interpreting changes in gene expression, a number of target physiological parameters have been measured over the last 3 years. Quantification of abscisic acid, sucrose, glucose, proline, relative water content and osmotic adjustment have been made in ear, silk and ear leaf tissues, at different times in a recombinant inbred line population. This work has been conducted in parallel with functional genomic activities to identify significant differences in gene expression that can be associated with target pathways. To consolidate the large amount of data generated through functional and structural approaches a unique linkage map has been constructed using the comparative map and trait viewer (CMTV) bioinformatics tool. Based on the frequency of significant regions identified across crosses or traits or both, a number of consensus regions have since been selected and these are currently being validated in a marker-assisted selection (MAS) experiment. It is clear, based on the progress made to date, that a multidisciplinary approach combining breeding, physiology and biotechnology is required for an effective understanding of a plant’s response to drought stress. The QTL information provides an essential bridge between data emerging from functional genomics approaches and responses of a plant at the morphological level. The colocalization on a linkage map between an expressed sequence tag (EST) that is differentially expressed and a QTL related to the same physiological parameter allows one to bridge the gap between plant phenotype and gene expression. Understanding the genetic basis of the essential morphological traits and physiological parameters of drought tolerance in maize should lead to new MAS strategies to improve the tolerance of maize and other crops to water-limited conditions.