The homeotic gene Ultrabithorax (Ubx) encodes homeodomain-containing transcription factors that determine segmental identity in Drosophila. Here, an immunopurification procedure is described that enriches for embryonic chromatin fragments containing binding sites for Ubx protein. In two cases these binding sites are located near embryonic transcription units regulated by the Ubx locus in vivo. Thus, these transcripts may correspond to Ubx target genes involved in elaborating segment-specific developmental pathways.