Background: It has been recommended that clinical trials on people with low back disorders (LBDs) should have a greater focus on subgroup specific treatment in order to increase the likelihood of clinically meaningful effects being demonstrated. Functional restoration is a treatment approach that has demonstrated some evidence of effectiveness in subacute and chronic LBDs. However, most studies to date have not used a clearly defined and appropriately detailed clinical protocol designed for and applied to a homogenous subgroup. Objectives: This paper presents a detailed classification and treatment protocol for people with a LBD and clinical features indicative of multifactorial persistent pain. The treatment is directed at psychosocial and neurophysiological barriers to recovery. Discussion: The classification and treatment components in the clinical protocol are discussed. Conclusion: The described clinical protocol will be used in the specific treatment of problems of the spine (STOPS) trials comparing specific physiotherapy to evidence-based advice.