This paper introduces the use of microarray data technology with the Agilent Maize Oligo Microarray (Design ID 016047) to characterize global changes in the transcript abundance of etiolated Zea mays (cv. Golden Cross Bantam) seedlings grown under microgravity (μg) conditions on the International Space Station (ISS) compared with those grown under 1 g conditions on Earth. Gene array data were analyzed according to stringent criteria that restricted the scored genes for specific hybridization values at least two fold. Of the 32152 - 32616 transcripts detected, 1030 and 590 transcripts were significantly different in the coleoptiles and in the mesocotyls. Of the transcripts detected, 877 and 428 transcripts were found to increase under μg conditions in the coleoptiles and the mesocotyls, respectively. Venn diagram analysis showed that 154 transcripts commonly increased and 10 decreased under μg conditions irrespective of the organ difference. Of these, phytohormone-related genes were focused, indicating that some of them were responsive to gravity. These results support the commonly accepted idea that phytohormone-related genes play a significant role in regulating plant growth and development under different gravity conditions.