The neural cell adhesion molecule L1, a member of the immunoglobulin superfamily, mediates cell interactions in the developing and regenerating nervous system of mammals and is also detectable in the immune system and in the epithelia of intestine, skin, lung, and kidney. This diverse pattern of expression begs the question as to the regulatory mechanisms underlying transcription of the L1 gene. We demonstrate here that the paired domain and homeodomain containing Pax-6 protein binds to three different sites in the promoter region of the L1 gene. The promoter proximal binding site is also recognized by Hoxa-1 and lies approximately 60 bp upstream from the transcription start site only few base pairs upstream of a putative binding site for the TFII-I transcription initiation factor. On the basis of this sequence, we have characterized the binding of Pax-6 and explored two modes of its DNA binding activities.