Water-deficit stress during meiosis is one of the most serious threats to crop production. To elucidate the mechanisms of the response to water-deficit stress in the reproductive organs of maize, we have characterized the changes in transcription that occur during meiosis in the tassels and floret formation in the ears following water deficit stress. We used oligo microarray analysis, which included 57,452 transcripts representing more than 30,000 identifiable unique maize genes, and combined this with reverse Northern blot analysis. After 7 days of stress, immature tassels and ears differed considerably in their transcriptional responses, and the majority of changes were organ specific. In the tassels, 1,513 transcripts were differentially expressed (by threefold or greater) with 62% of these being upregulated by water stress. In the ears, 202 transcripts were differentially expressed with 95% being upregulated by water stress. Most of these transcripts have not been previously reported to be associated with water stress. Only 74 of these transcripts were co-regulated in the two organs. The stress-regulated transcripts are involved in a broad range of cellular and biochemical activities. The most notable may function in carbohydrate metabolism, particular in sucrose, trehalose and raffinose metabolism, and in cell wall metabolism in the tassels. Collectively, these data suggest that the transcripts differentially expressed during reproductive organic development may represent candidate genes for dissecting molecular mechanism of this important biological process in response to water-deficit stress.