Deciphering mechanisms of early implantation of the embryo in cattle is of economical and fundamental interest, as these findings could help to reduce the implantation failure and also give clues regarding human sterility issues. One possible approach is to identify precisely the transcription factors (TF) responsible for gene expression in the uterus-conceptus dialogue. TF are proteins that interact directly with the DNA molecule by recognizing small and slightly degenerate nucleotide motifs (TFBS) in the promoter region of the genes The first issue is the accurate definition of promoter regions. In mammal, it is well known that the starting point for transcription of a gene (TSS) could be far from the translation start point, and that regulatory motifs can be found as far as several kb from the regulated gene. Regulatory annotation and comparison with orthologs could help to identify putative transcription start regions in cases where the biological information (EST, mRNA) is not available for cow. In the present work we propose the combination of several bioinformatic approaches to identify regulatory motifs in cattle promoters, we compare results from phylogenetic footprinting (footprinter) with orthologous genes from human, mouse and rat genomes, genetic algorithm (GALF-P) and statistical based motif search (Weeder) as the complete Bos taurus genome is now available. This pipeline will eventually be integrated in a platform allowing the analysis of datasets from high throughput transcriptomic analysis such as microarrays and ChIP-Seq, and is currently tested with previously annotated promoters dataset from milk regulatory genes.