Members of the homeobox gene superfamily of transcription factors are essential determinants of cellular identity during development. Their regulation and downstream gene targets are not well understood, however. This is due, in part, to the large number of genes that need to be analyzed simultaneously. A method has been developed for the rapid and simultaneous detection of changes in the expression of homeobox-containing genes, including members of the developmentally important Hox gene family. The method selectively amplifies and labels homeobox-containing mRNAs using a 3'-RACE procedure in combination with a degenerate forward primer that targets a highly conserved region of the homeobox found in all vertebrate Hox genes and many non-Hox homeobox-containing genes. The amplified sequences are identified by hybridization to a membrane-based array of covalently bound Hox and non-Hox homeobox gene sequences of interest. The method has been used here to demonstrate previously undetected changes in the expression of homeobox genes during retinoic acid-induced nerve cell differentiation in mouse pluripotent P19 cells. Published by Elsevier Inc.