The development of teeth through epithelial-mesenchymal interactions is mediated on a molecular level through the iterative and reciprocal action of secreted growth factors and responsive transcription factors. Although zinc finger transcription factors constitute by far the largest class of transcriptional regulators in mammals, little is known about their specific role in the regulation of tissue formation. The C2H2 zinc finger transcription factor Krox-26 is transiently expressed during organ formation, most prominently at sites of early tooth development and subsequently in secretory stage ameloblasts. The objective of this study was to determine the developmental expression pattern of Krox-26 during mouse embryogenesis and to determine its preferred DNA-binding site. Krox-26 protein expression could be detected in multiple tissues, most prominently in developing craniofacial structures. A target detection assay using recombinant Krox-26 protein identified the sequence CAATG as the preferred Krox-26 DNA-binding site. These results suggest that Krox-26 may regulate the expression of target genes through CCAAT box-related sequences in multiple tissues.