Cdx-2 is an intestine-specific homeodomain-containing transcription factor that activates the promoters of intestinal genes through specific interactions with the consensus, TTTAT/C. Here, we demonstrate that Cdx-2 interacts with the lactase-phlorizin hydrolase (LPH) promoter at cis-element (CE)-LPH1a (-54 to -40 bp) as well as the LPH TATA-box. Affinity comparisons between SIF-1, CE-LPH1a, and the LPH TATA-box revealed that the TATA-box has the lowest affinity for Cdx-2. Characterization of CE-LPH1a using EMSAs revealed binding of a novel, non-Cdx-2 complex in multiple cell lines that bind to sequence that is different from that of the Cdx-2 binding site. Heterologous promoter analysis in transient transfection assays revealed a repressor function for this protein, and thus, it was designated as nuclear factor-LPH1/repressor (NF-LPH1/R). These data are consistent with the hypothesis that NF-LPH1/R represses LPH gene expression in non-Cdx-2-producing cells, and that this repression is released in cells that synthesize Cdx-2, such as those in the intestinal epithelium. (C) 2002 Elsevier Science (USA). All rights reserved.