Many authors report changes in the control of the trunk muscles in people with low back pain (LBP). Although there is considerable disagreement regarding the nature of these changes, we have consistently found differential effects on the deep intrinsic and superficial muscles of the lumbopelvic region. Two issues require consideration; first, the potential mechanisms for these changes in control, and secondly, the effect or outcome of changes in control for lumbopelvic function. Recent data indicate that experimentally induced pain may replicate some of the changes identified in people with LBP. While this does not exclude the possibility that changes in control of the trunk muscles may lead to pain, it does argue that, at least in some cases, pain may cause the changes in control. There are many possible mechanisms, including changes in excitability in the motor pathway, changes in the sensory system, and factors associated with the attention demanding, stressful and fearful aspects of pain. A new hypothesis is presented regarding the outcome from differential effects of pain on the elements of the motor system. Taken together these data argue for strategies of prevention and rehabilitation of LBP.