Prediction of transcription factor binding sites (TFBS) is commonly used to formulate working hypotheses for experimental studies on gene regulation. Computational identification of functional TFBS is complicated because of short length and degeneracy of sequence motifs recognized by transcription factors. Information on conservation of predicted sites in orthologous sequences from different species (phylogenetic footprinting) can be used to distinguish potentially functional elements from background predictions. Results of phylogenetic footprinting may substantially depend on the algorithm used to construct an alignment of orthologous sequences, from which conservation of predicted TFBS is estimated. The CONREAL web server allows prediction and comparison of conserved TFBS based on AVID, BLASTZ, CONREAL, and LAGAN alignments. The web tool is particularly suited for the analysis of individual genes or genomic regions, although the underlying algorithm can also be used in high-throughput promoter analysis.