The mammalian cerebral cortex is organized in layers and columns, which are reflected in the local intrinsic connections and in the projections to and from the cortex. It is well established that the development of the columnar architecture is under the influence of neuronal activity, but little is known about the mechanisms that control the laminar specificity of cortical circuits. Here we review some recent studies which show that diffusible and membrane-associated molecules provide sufficient information to reconstruct layer-specific intrinsic and extrinsic cortical circuits under in vitro conditions.