<p>Abstract</p> <p>Background</p> <p>Iron (Fe) is the most limiting micronutrient element for crop production in alkaline soils. A number of transcription factors involved in regulating Fe uptake from soil and transport in plants have been identified. Analysis of transcriptome data from <it>Oryza sativa </it>grown under limiting Fe conditions reveals that transcript abundances of several genes encoding transcription factors are altered by Fe availability. These transcription factors are putative regulators of Fe deficiency responses.</p> <p>Results</p> <p>Transcript abundance of one nuclear located basic helix-loop-helix family transcription factor, <it>OsIRO3</it>, is up-regulated from 25- to 90-fold under Fe deficiency in both root and shoot respectively. The expression of <it>OsIRO3 </it>is specifically induced by Fe deficiency, and not by other micronutrient deficiencies. Transgenic rice plants over-expressing <it>OsIRO3 </it>were hypersensitive to Fe deficiency, indicating that the Fe deficiency response was compromised. Furthermore, the Fe concentration in shoots of transgenic rice plants over-expressing <it>OsIRO3 </it>was less than that in wild-type plants. Analysis of the transcript abundances of genes normally induced by Fe deficiency in <it>OsIRO3 </it>over-expressing plants indicated their induction was markedly suppressed.</p> <p>Conclusion</p> <p>A novel Fe regulated bHLH transcription factor (OsIRO3) that plays an important role for Fe homeostasis in rice was identified. The inhibitory effect of <it>OsIRO3 </it>over-expression on Fe deficiency response gene expression combined with hypersensitivity of <it>OsIRO3 </it>over-expression lines to low Fe suggest that OsIRO3 is a negative regulator of the Fe deficiency response in rice.</p