The maize inbred lines Huangzao 4 (HZ4) and Chang 7-2 (C7-2) are the foundation genotypes key to maize cross-breeding in China. C7-2 is derived from HZ-4. In this study, changes in phenotype, physiology and gene expression of three-leaf-old seedlings of HZ4 and C7-2 under the conditions of progressive water deficit (WD) and re-watering (RW) were compared to gain knowledge for breeding new maize foundation genotypes with higher drought tolerance. Progressive WD was produced by adding polyethylene glycol (PEG 6000) at 24 h intervals (24, 48 and 72 h) in Hoagland's nutrient solution, resulting in water potentials of -0.15, -0.3 and -0.5 MPa. The seedlings treated for 24 h at -0.5 [corrected] MPa were subjected to RW in the solution without complementation with PEG. The results showed that C7-2 seedlings are more tolerant to progressive WD than HZ4 seedlings in part because the former have a larger stomatal resistance, a relatively stronger leaf water-holding capacity, and a timely and stable increase in activities of antioxidant enzymes (superoxide dismutase and peroxidase) especially in roots upon WD. Oligonucleotide probe array-based analysis uncovered a number of WD- and RW-regulated genes in both inbred lines, and clearly indicated that fine transcriptional coordination between maize leaves and roots is one of the factors constituting higher WD tolerance and a greater ability for growth recovery from WD. On the basis of the resulting data and co-regulation of responsive genes in tissues, we propose a model for the whole maize plant tolerance to growth and recovery from WD.