In swine the phenotypical identification of regulatory T cells (Tregs) was limited so far to the surface expression of CD4 and CD25. However, with the discovery of the Treg-specific transcription factor forkhead-box p3 (Foxp3) in mice and humans a powerful marker for the identification of Tregs is available. Recently, we published data on a murine anti-mouse/rat Foxp3 antibody (FJK-16s) showing cross-reactivity with the putative porcine Foxp3 protein in lymphoid cells but the final proof for the specific cross-reactivity of this antibody was missing. By performing RACE-experiments, we have sequenced the entire porcine Foxp3 cDNA which is 1296 nucleotides in length and codes for a polypeptide of 432 amino acids. The porcine Foxp3 nucleotide and amino acid sequences show high homology to all known orthologues from other mammals, with the greatest homology with the bovine sequence. To demonstrate the specificity of the FJK-16s antibody for the porcine Foxp3 protein, HEK293T cells were transfected with porcine Foxp3 containing the FJK-16s-specific binding region and the expression of the epitope was identified by immuno-staining. In conclusion, this study represents the final proof for the specificity of the murine FJK-16s antibody for the porcine Foxp3 homologue and therefore strengthens future work on porcine Tregs.