Optimal function of the scapular stability system is considered to be an important feature in neck pain and the recurrence of neck pain. This study investigates the scapular stability system in patients with insidious onset neck pain and whiplash associated disorders by assessing whether there is a pattern of altered scapular orientation when the arm is resting by the side and during arm elevation. The onset of muscle activation of the scapular stability muscles; trapezius and serratus anterior, when the arm is elevated was also evaluated as well as the cervical-thoracic alignment. A control group was selected for comparison. The results revealed altered scapular orientation, altered cervical alignment and altered onset of muscle activation in the scapular stability muscles in the symptomatic groups. A different manifestation was revealed between the two symptomatic groups in scapular orientation. These changes in the scapular stability system and the alignment of the cervical spine may be an important mechanism for maintenance, recurrence or exacerbation of symptoms in patients with neck pain.