Cells in the mid-body region of the nematode C. elegans develop differently from their anterior or posterior homologs. The gene lin-39 is required for mid-body region-specific development. In lin-39 mutants, mid-body cells express fates characteristic of more anterior or posterior homologs, and the migration of a neuroblast through the mid-body is defective. lin-39 acts cell autonomously in these mid-body cells and in the migrating neuroblast. lin-39 encodes a protein with an Antennapedia class homeodomain, most similar to those of the Drosophila homeotic genes Deformed and Sex combs reduced, and is located in a homeotic gene cluster with two other regional homeotic genes, mab-5 and egl-5. lin-39 and mab-5 function combinatorially in 2 ectodermal cells and have redundant functions in gonad development.