Segmentation of the Drosophila embryo is controlled by a cascade of genes. Maternal genes provide the positional information along the longitudinal axis of the egg. Zygotic segmentation genes fall into the classes of gap, pair rule, and segment polarity genes which subdivide the longitudinal axis of the embryo into metameric units to be specified by the local activity of the homeotic genes. The activity of the maternal genes regulates the expression of the gap genes within distinct positions of the embryo by DNA-protein interactions. After expression in adjacent domains along the longitudinal axis of the embryo, the gap gene products form broad, overlapping protein gradients which provide the information to generate a periodic pattern of subordinate pair rule gene expression and to provide the spatial cues for the expression of homeotic genes. We show direct interaction of maternal gene products with gap genes, and gap gene products with a pair rule gene. Our data suggest that the generation of the pair rule expression pattern is due to concentration dependent interactions of gap gene products which act as transcriptional regulators on individual cis-acting pair rule gene elements.