Chlamydia spp. are obligate intracellular bacterial pathogens that alternate between two metabolically and morphologically distinct developmental forms, and differentiation depends on transcriptional regulation. Genome sequencing of Chlamydia trachomatis revealed an ORF, CT630 (chxR), whose amino acid sequence contains a winged helix-turn-helix motif similar to the DNA-binding domain of response regulators in the OmpR subfamily. ChxR differs from many response regulators in that essential residues in the receiver or phosphorylation domain are lacking. ChxR functions as a transcriptional regulator because it activated transcription of ompF and ompC when expressed in Escherichia coli. In vitro transcription combined with microarray analysis also demonstrated that ChxR activates its own expression by binding directly to sites upstream of chxR; it also activates infA, tufA, oppA, and CT084. DNase I protection studies showed that ChxR bound to sites in the ompF and ompC promoter proximal regions that overlap but were distinct from OmpR binding sites. Both proteins could bind simultaneously to their nonoverlapping binding sites. This report identifies a stage-specific transcriptional regulator and some of its target genes in Chlamydia.