Hox‐1.6, a mouse homeo‐box‐containing gene member of the Hox‐1 complex, is described. The Hox‐1.6 homeo‐box shows more divergence than the other members of the complex with the Drosophila Antennapedia‐like homeo‐box class. This previously undescribed gene was studied with respect to its transcription pattern and was found to be expressed during mouse fetal development in an intestine‐specific manner in adults, and in tumours or cell types exhibiting early endodermal‐like differentiation. The study of embryonic partial Hox‐1.6 cDNA clones revealed structural features common to other Drosophila and vertebrate homeo‐box‐containing genes, but also indicated that Hox‐1.6 transcripts might display splicing patterns more complex than those known for other vertebrate homeo‐genes. One of these cDNA clones contains a rather short open reading frame which would encode a protein of approximately 14.5 kd. The use of this clone as a probe for S1 nuclease mapping confirmed that different Hox‐1.6 transcripts were present both in embryonic total RNA and in embryonal carcinoma cell cytoplasmic RNA. These various transcripts are probably generated by an alternative splicing mechanism and may thus encode a set of related proteins.