The segment polarity gene cubitus interruptus (ci) is required to maintain expression of the wingless gene and to specify naked cuticle within each epidermal segment. Antibodies were generated against the ci protein and used to analyze its pattern of expression. By stage 11, post-transcriptional regulation of ci is observed. ci transcript levels are uniform across the anterior compartment, but protein levels are higher next to the compartment boundaries. The distribution of the ci protein is altered in fused, hedgehog and wingless mutants suggesting cell-cell signaling may regulate ci protein levels. The role of ci in cell-cell signaling and pattern formation was examined in double mutants of ci with patched and zeste-white3/shaggy.