Although the diversity of neocortical and hippocampal GABAergic interneurons is recognized in terms of their anatomical, molecular and functional properties, principal cells are usually assumed to constitute homogenous populations. However, even within a single layer, subpopulations of principal cells can often be differentiated by their distinct long-range projection targets. Such subpopulations of principal cells can have different local connection properties and excitatory inputs, forming subnetworks that may serve as separate information-processing channels. Interestingly, as reviewed here, recent evidence has revealed specific instances where interneuron cell types selectively innervated distinct subpopulations of principal cells, targeting only those with particular long-distance projection targets. This organization represents a novel form of interneuron specialization, providing interneurons with the potential to selectively regulate specific information-processing streams.