The zinc finger protein CTCF has been shown to mediate multiple functions connected to gene repression. Transcriptional inhibition as well as enhancer blocking and chromatin insulation are documented for CTCF in men, mice and chickens. Additionally, hCTCF has been linked to epigenetics and disease. In line with these basic cellular functions, CTCF has been found to be expressed in every cell type and adult tissue tested and has thus been deemed an ubiquitous protein. Here, we report the identification of the CTCF homologue from Xenopus and the analysis of the spatio-temporal expression of xCTCF during embryogenesis. Within the DNA binding domain, xCTCF is virtually identical to other identified vertebrate CTCF proteins. Homology also extends to other conserved regions that are important for CTCF function. Although xCTCF mRNA is present during all stages of early Xenopus development, a remarkable increase in expression is observed in neuronal tissues. Early in development, xCTCF is highly expressed in the neural plate and later in the neural tube and developing brain. By tailbud stage, elevated expression is also seen in the developing sensory organs of the head. This is the first detailed description of the expression pattern of a vertebrate insulator protein during embryogenesis.