Various Hox genes are known to produce alternative transcripts encoding different isoforms whose physiological relevance during development is not yet understood. In this work, we analysed two different Hoxa9 mRNAs encoding a full-length protein (Hoxa9) or a protein lacking the homeodomain (Hoxa9T). First, we demonstrated that these transcripts are conserved from birds to mammals. We then showed that both transcripts are present throughout embryogenesis and that Hoxa9T transcript is particularly abundant in embryonic genital tract, kidney, forelimb and tail. We further found that both isoforms are able to interact with CBP, suggesting a competition between Hoxa9 and Hoxa9T with this protein.