Regionally distinct elongation responses to water stress in the maize primary root tip have been observed in the past. A genetic basis for such differential responses has been demonstrated. Normalized bar-coded cDNA libraries were generated for four regions of the root tip, 0-3 mm (R1), 3-7 mm (R2), 7-12 mm (R3), and 12-20 mm (R4) from the root apex, and transcript profiles for these regions were sampled. This permitted a correlation between transcript nature and regional location for 15 726 expressed sequence tags (ESTs) that, in approximately equal numbers, derived from three conditions of the root: water stress (water potential: -1.6 MPa) for 5 h and for 48 h, respectively, and well watered (5 h and 48 h combined). These normalized cDNA libraries provided 6553 unigenes. An analysis of the regional representation of transcripts showed that populations were largely unaffected by water stress in R1, correlating with the maintenance of elongation rates under water stress known for R1. In contrast, transcript profiles in regions 2 and 3 diverged in well-watered and water-stressed roots. In R1, transcripts for translation and cell cycle control were prevalent. R2 was characterized by transcripts for cell wall biogenesis and cytoskeleton formation. R3 and R4 shared prevalent groups of transcripts responsible for defence mechanisms, ion transport, and biogenesis of secondary metabolites. Transcripts which were followed for 1, 6, and 48 h of water stress showed distinct region-specific changes in absolute expression and changes in regulated functions.