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The AAAP (amino acid/auxin permease) genes encode a large family of transporters. A few members of the AAAP family have been characterized in Arabidopsis thaliana and rice (Oryza sativa). However, little is known about AAAP genes in maize (Zea mays). Therefore, we performed a systematic bioinformatics analysis to characterize all AAAP genes in maize, which included analysis of the genome sequence, conserved protein domains, chromosomal locations, phylogenetic relationships, gene duplications, and gene expression profiles. In this study, seventy-one ZmAAAP genes were identified and named ZmAAAP01 to ZmAAAP71. The number of AAAP genes in maize is more than the number in Arabidopsis thaliana (43) and in rice (58). We found a higher percentage of AAAP gene duplications in the maize genome, which contributed to the expansion of the AAAP gene family. Furthermore, segmental duplications played a major role in the AAAP gene expansion in maize. The AAAP genes are unevenly distributed on the 10 maize chromosomes, and 31 of them are distributed within 12 clusters on segmental chromosomes. Both the EST analysis and transcriptome data indicated that most ZmAAAP genes exhibited abundant expression patterns, suggesting diverse and novel functions of AAAP gene family in maize. The results presented here provide useful information for further functional analysis of the AAAP gene family in maize.