Analogous to the neural code, which is a model that characterizes the relationships between brain activity and sensory input and motor output, the connectome code is a model that characterizes the relationship between brain structure and brain or body activities, encoded in either plasticity or development. We describe the basic statistical formulation and motivation for the connectome code, while providing a number of examples across the phylogenetic spectrum as well as experimental modalities spanning spatiotemporal scales. Connectome coding is an emerging sub-discipline in neuroscience with many open opportunities.