Molecular changes caused by sensory trauma and subsequent structural alterations of the central nervous system are only beginning to be identified. In most cases, the generation of tinnitus can be linked to damage of the peripheral auditory system, probably even in cases where hearing impairment cannot be assessed by audiometry. Within a common view, acoustic trauma and salicylate induce abnormal excitability at the level of the brainstem, subcortical and cortical level that may be related to tinnitus. The present review summarizes studies emphasizing a crucial role of molecular events that occur in the cochlea exhibiting the potential to alter the network activity in distinct areas of the brain, including the limbic system. We proceed from the inner ear to the auditory cortex and discuss the recent molecular findings in the central auditory system as a secondary step of previous neuronal changes in the periphery.