Abstract Mutations in the pair-rule class of segmentation genes cause pattern deletions with a double segment periodicity in the Drosophila embryo. This phenotype is, in part, due to cell death. Using molecular probes for engrailed (en) and Ultrabithorax (Ubx) expression as markers for the body plan, we have studied the phenotype of pair-rule mutants prior to cell death. All these mutants alter the expression of en and Ubx; then-molecular phenotypes suggest a pathway whereby pair-rule gene functions construct metameric units.