Faecal incontinence can affect as many as 1 in 10 of the population and increases in prevalence as we age. In most cases this can lead to social isolation, reduced quality of life and depression. Despite this, faecal incontinence therapies remain controversial, with limited evidence base and little in the way of objective scientific criteria. Maintenance of faecal continence is complex and involves coordination of the anorectum and pelvic floor via intricate motor and sensory neural pathways. And while the major component in this process is the anal sphincter, faecal continence depends not only on sphincter integrity but also on spinal and cerebral inputs to the pelvic floor. Given this anatomical insight, it is surprising that the neurophysiological mechanisms which control human anal continence remain uncertain. A better understanding of these neurophysiological processes may therefore help in elucidating the pathophysiology of faecal incontinence, as well as guide management. In this talk, I will examine present knowledge about the cortical control of anal function in man particularly from investigations with Transcranial Magnetic Stimulation, and explore what aspects of its organisation are influenced by peripheral/spinal inputs. In addition, I will describe current approaches to faecal incontinence therapies and review the evidence base for such interventions. Finally I will discuss new approaches for the rehabilitation of faecal incontinence that might harness compensatory brain mechanisms to improve sphincter function.