The major excitatory, binaural inputs to the central nucleus of the inferior colliculus (ICC) are from two groups of neurons with different functions—the ipsilateral medial superior olive (MSO) and the contralateral lateral superior olive (LSO). A major inhibitory, binaural input emerges from glycinergic neurons in the ipsilateral LSO. To determine whether these inputs converge on the same postsynaptic targets in the ICC, two different anterograde tracers were injected in tonotopically matched areas of the MSO and the LSO on the opposite side in the same animal. The main findings were that the boutons from MSO axons terminated primarily in the central and caudal parts of the ICC laminae but that contralateral LSO terminals were concentrated more rostrally and on the ventral margins of the MSO inputs. In contrast, the ipsilateral LSO projection converged with the MSO inputs and was denser than the contralateral LSO projection. Consistent with this finding, retrograde transport experiments showed that the very low-frequency areas of the ICC with dense MSO inputs also received inputs from greater numbers of ipsilateral LSO neurons than from contralateral LSO neurons. The results suggest that different binaural pathways through the low-frequency ICC may be formed by the segregation of excitatory inputs to ICC from the MSO and the contralateral LSO. At the same time, the ipsilateral LSO is a major inhibitory influence in the target region of the MSO. These data support the concept that each frequency-band lamina in the ICC may comprise several functional modules with different combinations of inputs. J. Comp. Neurol. 472:330–344, 2004. © 2004 Wiley-Liss, Inc.