To acquire iron (Fe), graminaceous plants secrete mugineic acid family phytosiderophores through the phytosiderophore efflux transporter TOM1 and take up Fe in the form of Fe(III)-phytosiderophore complexes. Yellow stripe 1 (ys1) and ys3 are recessive mutants of maize (Zea mays L.) that show typical symptoms of Fe deficiency, i.e., interveinal chlorosis of the leaves. The ys1 mutant is defective in the Fe(III)-phytosiderophore transporter YS1 and is therefore unable to take up Fe(III)-phytosiderophore complexes. While the ys3 mutant has been shown to be defective in phytosiderophores release, the causative gene has not been identified. The present study was performed to characterize the expression profiles of the genes in ys1 and ys3 mutants to extend our understanding of Fe homeostasis in maize. Using quantitative real-time polymerase chain reaction, we assessed changes in the levels of gene expression in response to Fe deficiency of genes involved in Fe homeostasis, such as those related to phytosiderophore biosynthesis and Fe transport. As with other crops, these Fe deficiency-inducible genes were also upregulated in maize. In addition, these Fe deficiency-inducible genes were upregulated in both the ys1 and ys3 mutants, even under Fe-sufficient conditions. Indeed, the Fe concentrations in the roots of ys1 and ys3 plants were lower than that of wild-type controls. These results suggest that ys1 and ys3 are Fe-deficient during growth in the presence of Fe. In agreement with previous reports, the level of YS1 expression decreased in the ys1 mutant. Moreover, the expression level of a homolog of TOM1 in maize decreased significantly in the ys3 mutant. Unspliced introns of ZmTOM1 were detected only in ys3, and not in YS1YS3 or ys1, suggesting that ZmTOM1 may be involved in the ys3 phenotype.