Annexins have previously been identified and characterized in 'Arabidopsis' and rice. They compose a multigene family in plants. In this study, we indicated the isolation and characterization of maize annexin genes across a whole genome using bioinformatics, microarray and real-time PCR methods. A total of 12 members of this family were identified in the maize genome. The 12 maize annexins were distributed on eight maize chromosomes. Multiple alignment and motif display results revealed that most maize annexin proteins contained 1-4 annexin repeats. A phylogenetic analysis indicated the maize annexin gene family could be divided into four subfamilies. In brief, putative cis-elements involved in abiotic stress response, phytohormones, pollen-specific elements and seed development were observed in the promoters of maize annexin genes. Microarray data showed that the maize annexin genes had tissue-specific expression patterns in the maize developmental steps. The QRT-PCR analysis result indicated that all 12 genes were induced in the seedling leaves by PEG and NaCl.