The maternal morphogen Bicoid (Bcd) is distributed in an embryonic gradient that is critical for patterning the anterior-posterior (AP) body plan in Drosophila. Previous work identified several target genes that respond directly to Bcd-dependent activation. Positioning of these targets along the AP axis is thought to be controlled by cis-regulatory modules (CRMs) that contain clusters of Bcd-binding sites of different ''strengths.'' Here we use a combination of Bcd-site cluster analysis and evolutionary conservation to predict Bcd-dependent CRMs. We tested 14 predicted CRMs by in vivo reporter gene assays; 11 show Bcd-dependent activation, which brings the total number of known Bcd target elements to 21. Some CRMs drive expression patterns that are restricted to the most anterior part of the embryo, whereas others extend into middle and posterior regions. However, we do not detect a strong correlation between AP position of target gene expression and the strength of Bcd site clusters alone. Rather, we find that binding sites for other activators, including Hunchback and Caudal correlate with CRM expression in middle and posterior body regions. Also, many Bcd-dependent CRMs contain clusters of sites for the gap protein Kruppel, which may limit the posterior extent of activation by the Bcd gradient. We propose that the key design principle in AP patterning is the differential integration of positive and negative transcriptional information at the level of individual CRMs for each target gene.morphogen ͉ network ͉ transcription G radients of two transcription factors, Bicoid (Bcd) and Dorsal (Dl), are critical for patterning the major body plan axes in the Drosophila embryo. This studied focused on Bcd, a maternal effect gene whose mRNA is initially localized at the anterior pole of the oocyte (Fig. 1A) (1). Upon egg deposition, the trapped bcd RNA is translated, and a nuclear gradient forms, with highest concentrations near the anterior pole and progressively lower concentrations in more posterior regions (Fig. 1B) (2). Bcd protein distribution matches its biological activity, with high levels required for the positioning of the most anterior structures, intermediate levels for head structures, and low levels for the thoracic and anterior abdominal segments. Varying the shape of the Bcd gradient has a direct effect on positional identity in the blastoderm (3). Increasing the maternal input of bcd can shift morphological landmarks posteriorly, whereas decreasing it shifts them anteriorly. These experiments suggest that the concentration of Bcd protein present at each position along the length of the embryo (EL) determines the destiny of cells that will occupy that region.Bcd protein contains a homeodomain and functions as a morphogen by activating the transcription of multiple target genes in different positions along the anterior-posterior (AP) axis (reviewed in refs. 4 and 5). Driever, Thoma, and Nüsslein-Volhard (6) first proposed that differential positioning could occur by means of gene-specific regulatory ele...