The establishment of synaptic connections is essential for normal brain function, yet the molecular mechanisms responsible for the precise connectivity of specific neural circuits remain largely unknown. Previous work has shown that the assembly of cortical circuits requires specific functions of molecular signalling complexes at different classes of synapses. In this talk, I will describe the molecular logic through which specific pyramidal cell-interneuron circuits are established in the cerebral cortex of the mouse, and how alterations in some of these connectivity motifs might be liked to disease.