The invected and engrailed genes are juxtaposed in the Drosophila genome and are closely related in sequence and pattern of expression. The structure of the most abundant invected transcript was defined by obtaining the full-length cDNA sequence and by S1 nuclease sensitivity and primer extension studies; a partial sequence of the invected gene was determined; and the developmental profile of invected expression was characterized by Northern analysis and by in situ localization. The invected gene, like the engrailed gene, is expressed in the embryonic and larval cells of the posterior developmental compartments and in the embryonic hindgut, clypeolabrum, and nervous system. Like the engrailed gene, the invected gene can encode a protein of approximately 60 kD that contains a homeo box near its carboxyl terminus; indeed, a sequence of 117 amino acids in the carboxy-terminal region of both proteins is almost identical. The developmental role of the invected gene is not known.