Resistance to drought in plants clearly is not a simple trait, but a complex of mechanisms working in combination to avoid or to tolerate water deficits. All physiological, morphological and developmental changes that confer drought tolerance in plants must have a molecular genetic basis. Thus, genotypes which differ in tolerance to water stress should have qualitative or/and quantitative differences in gene expression. To identify and isolate genes which may differ among four cotton genotypes with diverse responses to water deprivation, we used Differential Display (DD). A total of 109 cDNA fragments differentially displayed were identified. These fragments were extracted from the DD gels and reamplified. Sixty five reamplified fragments were cloned in pGEM-T vectors and sequenced. GeneBank searches showed 17 clones with high homology to known genes, and 20 clones with low homology, while 15 clones had no homologous entries. Ribonuclease protection assays (RPA) were used to confirm expression of most of the interesting differentially displayed fragments. These fragments can be used as riboprobes to screen germplasm banks to identify genotypes presenting similar water-deficit tolerance characteristics found in the genotypes used in this study.