Growth, yield, and yield quality of cotton are greatly affected by water-deficit stress. We have identified the genes and associated metabolic pathways involved in the water-deficit stress response in leaf and root. Gene expression profiles were developed for leaf and root tissues subjected to slow-onset water deficit under controlled, glasshouse conditions. The water-deficit stress was characterized by leaf water potential of -23.1 bars for stressed tissue compared to -8.7 bars for fully-irrigated control plants and a corresponding decrease in net carbon assimilation to approximately 60% of the rates seen in the irrigated controls (30.3 ± 4.7 μmol CO(2) m(-2) s(-1) compared to 17.8 ± 5.9 μmol CO(2) m(-2) s(-1)). Profiling experiments revealed 2,106 stress-responsive transcripts, 879 classified as stress-induced, 1,163 stress-repressed, and 64 showed reciprocal expression patterns in root and leaf. The majority of stress-responsive transcripts had tissue-specific expression patterns and only 173 genes showed similar patterns of stress responsive expression in both tissues. A variety of putative metabolic and regulatory pathways were identified using MapMan software and the potential targets for candidate gene selection and ectopic expression to alter these pathways and responses are discussed.