Synapse elimination and strengthening are central mechanisms for the developmental organization of excitatory neuronal networks. Little is known, however, about whether these processes are also involved in establishing precise inhibitory circuits. We examined the development of functional connectivity before hearing onset in rats in the tonotopically organized, glycinergic pathway from the medial nucleus of the trapezoid body (MNTB) to the lateral superior olive (LSO), which is part of the mammalian sound localization system. We found that LSO neurons became functionally disconnected from approximately 75% of their initial inputs, resulting in a two-fold sharpening of functional topography. This was accompanied by a 12-fold increase in the synaptic conductance generated by maintained individual inputs. Functional elimination of MNTB-LSO synapses was restricted to the period when these glycinergic/GABAergic synapses are excitatory. These results provide new insights into the mechanisms by which precisely organized inhibitory circuits are established during development.