The rice Xa13 gene, whose promoter harbors a UPT (up-regulated by transcription activator-like [TAL] effector) box, UPT(PthXo1), plays a pivotal role in the race-specific pathogenicity caused by Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99. PXO99 causes rice disease by inducing Xa13. It is unknown, however, whether the UPT(PthXo1) box is the only PXO99-responsive cis-regulating elements in the activation of Xa13 expression. We analyzed the expression of a series of end- and site-truncated and site-mutated Xa13 promoters in rice and the binding of PXO99 protein to the intact, partial, or site-mutated UPT(PthXo1) boxes. In the Xa13 promoter, UPT(PthXo1) box is the only Xoo-responsive cis-acting element that results in PXO99-induced Xa13 expression. The 5'-terminal second, third, and fourth nucleotides of the box are important for bacterial protein binding and gene activation; mutation of any one of these sites abolished PXO99-induced gene expression. Furthermore, the 3'-half of the UPT(PthXo1) box is also required for protein binding and gene activation. These findings will enhance our understanding of the molecular mechanism of the interaction of rice and Xoo via UPT boxes and TAL effectors.