THE segmentation of the Drosophila body plan depends on a hierarchy of interactions among ˜20–25 regulatory genes that are active in the early embryo (refs 1–4; for a review see ref. 5). The gap genes have a key role in this process and are responsible for the periodic expression of certain pair-rule genes^6–8 and the localized expression of several homoeotic genes^9–11. The two best characterized gap genes, hunchback (hb) and Krüppel (Kr) contain homologies with the zinc-finger DNA-binding motif^12,13, although their mode of action in the early embryo is unknown. Here we report that both of the proteins encoded by these genes possess sequence-specific DNA-binding activities, which indicates that they might regulate gene expression at the level of transcription. The binding sites of the hb gene product are related by a 10-base pair (bp) consensus sequence, ^G/A_C/CTAAAAAA, whereas the binding sites of the Kr gene product share a distinct 10-bp motif, AACGGGTTAA. It is possible that the hb and Kr proteins cooperatively regulate gene expression, because they are expressed in broad, overlapping gradients in the early embryo. We also provide evidence that the on/off periodicity of the pair-rule gene even-skipped (eve) ^14,15 involves the interaction of the hb and Kr proteins with defined eve promoter elements^16,17.