Clinical theory suggests that altered alignment of the shoulder girdle has the potential to create or sustain symptomatic mechanical dysfunction in the cervical and thoracic spine. The alignment of the shoulder girdle is described by two clavicle rotations, i.e, elevation and retraction, and by three scapular rotations, i.e., upward rotation, internal rotation, and anterior tilt. Elevation and retraction have until now been assessed only in patients with neck pain. The aim of the study was to determine whether there is a pattern of altered alignment of the shoulder girdle and the cervical and thoracic spine in patients with neck pain. A three-dimensional device measured clavicle and scapular orientation, and cervical and thoracic alignment in patients with insidious onset neck pain (IONP) and whiplash-associated disorder (WAD). An asymptomatic control group was selected for baseline measurements. The symptomatic groups revealed a significantly reduced clavicle retraction and scapular upward rotation as well as decreased cranial angle. A difference was found between the symptomatic groups on the left side, whereas the WAD group revealed an increased scapular anterior tilt and the IONP group a decreased clavicle elevation. These changes may be an important mechanism for maintenance and recurrence or exacerbation of symptoms in patients with neck pain.