Sugarcane crop is of large economic importance in the tropical and subtropical regions, especially in some countries of Central and South America as Brazil, which is actually the major worldwide producer. The limitation of water availability is a major factor influencing plant growth and crop production. Using cDNA macroarray technology we determine the expression profile of several ESTs (expressed sequence tags) with higher similarity to the enzymes involved in the biosynthesis of proline, hydroxyproline, GABA (g-amino butyric acid) and antioxidant defense in two sugarcane cultivars (Saccharum spp), one water stress tolerant (SP83-2847) and other water stress sensitive (SP90-1638). Both cultivars were submitted two water-deficit levels mild (T1) and severe (T2). Our results showed for the tolerant cultivar up-regulated ESTs similar to genes that belong to biosynthetic pathways of proline, hydroxyproline and GABA and ESTs for antioxidant defense systems that were down-regulated. For the sensitive cultivar instead, the ESTs for the proline, hydroxyproline and GABA biosynthetic pathway are down-regulated and up-regulated for the antioxidant defense system. A possible explanation of these results was discussed and we propose a molecular model for the possible sugarcane response to drought.