Physically linked Dlx5 and Dlx6 paralogs are co-expressed in vertebrates and various combinations of null alleles in mice demonstrate not only functional redundancy between the paralogous factors but a similar quantitative contribution to craniofacial functions during development. While it is not possible to rule out that the bigene pair contributes some paralog-specific functions it is clear that, for many functions in the head, Dlx5 and Dlx6 are interchangeable. To assess the relative quantitative contribution made by each paralog to bigene function, we have made comparisons of the expression of Dlx5 and Dlx6 in chick embryos and quantitated the transcriptional properties of the encoded proteins in a variety of regulatory and cellular contexts. Our data indicate that the transcriptional activities of both Dlx5 and Dlx6 are very much context dependent; isolated domains fused to a heterologous DNA binding domain have little intrinsic activity, while individual domains are more active when contiguous with their own homeodomain. We find Dlx5 and Dlx6 to be quantitatively indistinguishable on a variety of natural cis-regulatory sequences in a heterologous cellular context but observed quantitatively different transcriptional outputs in cells that normally express these genes, suggesting differential interactions with co-evolved co-activators. (C) 2016 Elsevier Inc. All rights reserved.