Maize female organs are sensitive to drought stress, leading to reproductive failure and yield reduction. In the present study gene expression profiles of ears and silks of maize at the flowering stage under drought stress were investigated. From 1920 white positive clones of a forward suppression subtractive hybridization (SSH) library, 1439 available sequences of expression sequence tags (ESTs) were obtained, resulting in 361 unique ESTs after assembling. Data analysis showed that 218 of the unique ESTs had significant protein homology by BLASTX in UNIPROT database. Totally 99 uniESTs were found in TIGR maize gene indices and nr database by BLASTN, while 44 uniESTs were not found to have homologous nucleic acid sequences and putatively classified as "maize-specific" uniESTs. The 218 cDNAs with significant protein homology were sorted into 13 groups according to the functional categories of the Arabidopsis proteins. Among those genes, the genes associated with the metabolisms were the largest group (account for 27%), and the genes related to protein synthesis, protein fate, transcription, cell cycle and DNA processing accounted for 16, 10, 10 and 9%, respectively. After analysis of macroarray data and real-time quantitative polymerase chain reaction (PCR), it was found that 160 of the 218 homologous protein uniESTs were up-regulated genes in the ears, 129 in the silks, and 125 in both of the tissues. The present work provided a valuable starting point for further elucidation of the roles played by these genes/gene products in drought tolerance in maize.