Understanding how regulatory networks initiate, maintain and synchronise transcriptional states remains a fundamental goal of developmental biology. Complex patterns of spatio-temporal gene expression are generated through the combined inputs of signalling and transcriptional networks converging on cis-regulatory modules (CRMs). Detailed studies in Drosophila, using transgenic reporter assays and mutagenesis analysis, have dissected the regulatory logic of a number of CRMs. These data have recently been complemented by genome-wide maps of transcription factor binding, revealing an unprecedented view of CRM occupancy and network complexity. The synthesis of data for three well-characterised Drosophila developmental networks reveals emerging themes at both a CRM and a cis-regulatory network level.