Back and neck pain are common conditions that have a high burden of disease. Changes in somatosensory function in the periphery, the spinal cord and the brain have been well documented at the time when these conditions have become chronic. It is unknown, however, how early these changes occur, what the timecourse is of sensory dysfunction and what the specific nature of these changes are in the first 12 weeks after onset of pain. In this paper, we describe the protocol for a systematic review of the literature on somatosensory dysfunction in the first 12 weeks after pain onset. We will conduct a comprehensive search for articles indexed in the databases Ovid MEDLINE, Ovid Embase, Ovid PsycINFO and Cochrane Central Register of Controlled Trial (CENTRAL) from their inception to August 2013 that report on any aspect of somatosensory function in acute or subacute neck or back pain. Two independent reviewers will screen studies for eligibility, assess risk of bias and extract relevant data. Results will be tabulated and a narrative synthesis of the results conducted. Currently, there is a gap in our knowledge about the timing of somatosensory changes in back and neck pain. The systematic review outlined in this protocol aims to address this knowledge gap and inform developments in diagnostic tools and pain mechanism-based treatments. Our protocol has been registered on PROSPERO, CRD42013005113.