The segmented body pattern of the Drosophila embryo is established through a hierarchical network of interacting genes. At each successive step in this pathway, transcriptional regulation is used to convert coarse positional information into finer patterns of gene expression. Central to this process are the cis-regulatory regions that drive the dynamic spatial expression of the different segmentation genes. Here we describe the cis-regulatory region of the runt gene. As found for both other primary pair-rule genes, hairy and even-skipped, there are stripe-specific elements which mediate the initial regulation of runt stripes by gap genes. We did not find autoregulatory elements as described for even-skipped and fushi tarazu. The regulation of runt by other pair-rule genes is mediated by a large region, extending over 5 kb upstream and downstream of the transcription start site. This "disperse" element cannot be subdivided into functionally independent subelements or minimal elements. Such disperse elements mediating pair-rule gene interactions may have escaped detection in other segmentation genes and may involve molecular mechanisms different from those mediating regulation by gap genes.