In vertebrate nervous systems, different classes of synaptic inputs are often segregated into restricted compartments of target neurons. For example, distinct types of GABAergic interneurons preferentially innervate subcellular domains and have been implicated in the precise temporal regulation of integration within neurons and activity within networks. Recent studies suggest that the subcellular segregation of different classes of GABAergic synapses is largely genetically determined. The localization and signaling of L1 family immunoglobulin proteins recruited by ankyrin-based membrane adaptors might serve as compartmental labels, which contribute to subcellular synapse organization in cerebellar Purkinje neurons.