Deficits in motor coordination of the trunk muscles have been extensively reported in individuals with chronic low back pain. Many of these changes in coordination persist after the resolution of symptoms and a failure to recover control of the trunk muscles is associated with increased recurrence of pain episodes. Notably, clinical trials demonstrate that motor training of the trunk muscles leads to reduced low back pain intensity, decreased disability and reduced recurrence of pain episodes. However, it remains unclear whether changes in motor coordination, which is the target of motor training programs, can be induced with specific training of the trunk muscles. Furthermore, little is known about the organisation of control of the trunk muscles in the central nervous system, the potential for plastic changes with pain and injury, and the potential for recovery or its mechanisms. The overall aim of this thesis was to investigate the organisation of inputs to the trunk muscles in the central nervous system, and to examine whether changes in this organisation, particularly at the motor cortex, are related to alterations in motor coordination following pain and motor training.Recordings of electromyographic activity of the trunk and limb muscles were made using a combination of surface and intramuscular fine wire electrodes. Motor coordination of the trunk muscles was examined through a series of reactive, postural and functional tasks. Transcranial magnetic stimulation was used to investigate the excitability and representation of motor cortical cells that project to the trunk muscles. There were several novel findings. The studies showed that deficits in motor coordination of the trunk muscles were associated with changes in its organisation at the motor cortex in individuals with chronic low back pain. Importantly, the results revealed that motor training could induce improvements in the coordination of the trained muscle during postural tasks, and that this improvement could be partly explained by plastic changes at the motor cortex. In addition, the data also revealed important findings that relate to the organisation of the trunk muscles at the central nervous system and contribute to the understanding of how these muscles are controlled during postural and functional tasks. Together, these studies unravelled some of the neurophysiological mechanisms that help to explain changes in motor coordination with pain and following motor training.Notably, these findings provide further evidence that supports the efficacy of motor training interventions for the rehabilitation of patients with low back pain.