Understanding how the cochlea works as a system has become increasingly important. We need to know this before integrating new information from genetic, physiological and clinical sources. This chapter will show how the cochlea should be seen as a device for carrying out a frequency analysis built from cells that have been adapted for specialist purposes. Sensory hair cells convert mechanical displacements into the neural code. The transducer channel remains to be identified. The biomechanics of the cochlear duct depends on an energy-dependent feedback from the sensory outer hair cells. The molecular basis for outer hair cell feedback depends on a protein that has recently been identified. The auditory signal encoded by the cochlea is further modified by membrane properties of the hair cells and cochlear supporting cells. The interplay between techniques of genetics, molecular biology and cell physiology has started to reveal which ion channels and transporters in the cochlea are mutated in certain forms of deafness. The interpretation of these mutations requires the cell physiology of the cochlear partition to be better characterised in the future.