The cerebral cortex is subdivided into discrete functional areas that are defined by specific properties, including the presence of different cell types, molecular expression patterns, microcircuitry and long-range connectivity. These properties enable different areas of cortex to carry out distinct functions. Emerging data argue that the particular structure and identity of cortical areas derives not only from specific inputs but also from unique processing networks. The aim of this review is to summarize current information on the interplay of intrinsic molecular cues with activity patterns that are driven by sensory experience and shape cortical networks as they develop, emphasizing synaptic connections in networks that process vision. This review is part of the TINS special issue on The Neural Substrates of Cognition.