Background: Recent experimental research has suggested that spinal manipulative therapy (SMT) may reduce pain through modulation of the ascending pain signals and/or the central pain-regulating mechanisms. People with persistent neck pain (NP) have also been found to have disturbances in autonomic nervous system (ANS) regulation. A common way to study the ANS is to measure heart rate variability (HRV). It is not known whether deviations in HRV are related to changes in pain perception or to the treatment response to SMT. Commonly, an individual in pain will experience pain reduction when exposed to a second pain stimulus, a mechanism known as conditioned pain modulation (CPM). Patients with persistent pain have been found to have a reduced CPM reaction. It is not known whether this is predictive of treatment response to SMT. The aim of the study is to examine the effects of SMT on HRV and pain. Further, a secondary aim is to test whether a CPM test can be used to predict treatment response in a population of patients with recurrent and persistent NP.Method/design: A multicentre randomized controlled clinical trial will be carried out in multidisciplinary primary care clinics. This setting is chosen to minimize bias resulting from patient preference for the treatment modality and provider. The subjects are either self-referred or referred from other health care practitioners locally. The treatment modalities are two well-known interventions for NP; SMT and stretching exercises compared to stretching exercises alone. HRV will be measured using a portable heart monitor. The subjective pain experience will be investigated by assessing pain intensity and the affective quality of pain. CPM will be measured with a standardized cold pressor test. Measurements will be performed three times during a 2-week treatment series.Discussion: The study will utilize normal clinical procedures, which should aid the transferability and external validity of the results. The study will provide knowledge regarding the underlying mechanisms of the effects of SMT. Furthermore, the study will examine whether a CPM test is predictive of treatment outcome in a population of patients with recurrent and persistent NP.