Engrailed is required to establish and maintain developmental compartments within each segment of the fly. To understand the role of the engrailed protein in this process, we have raised antibodies against engrailed and have visualized an engrailed protein in embryos by indirect immunofluorescence. The protein accumulates in the nucleus, supporting the notion that engrailed is a regulatory factor. The first pattern of expression is in alternating segments followed by expression in every segment, suggesting that engrailed may be responding to pair-rule segmentation gene products. Overall, engrailed protein levels peak in areas undergoing morphogenesis. Finally, the complex final form of the head and terminalia derive from earlier simple subdivision of these areas into developmental fields by engrailed.