Although it is known that responses in the auditory cortex are evoked predominantly contralateral to the side of stimulation, the lateralization of responses at lower levels in the human central auditory system has hardly been studied. Furthermore, little is known on the functional interactions between the involved processing centers. In this study, functional MRI was performed using sound stimuli of varying left and right intensities. In normal hearing subjects, contralateral activation was consistently detected in the temporal lobe, thalamus and midbrain. Connectivity analyses showed that auditory information crosses to the contralateral side in the lower brainstem followed by ipsilateral signal conduction towards the auditory cortex, similar to the flow of auditory signals in other mammals. In unilaterally deaf subjects, activation was more symmetrical for the cortices but remained contralateral in the midbrain and thalamus. Input connection strengths were different only at cortical levels, and there was no evidence for plastic reorganization at subcortical levels.