Patients with whiplash associated disorders (WAD) have shown less accuracy in trajectory head motion compared to asymptomatic controls, which comply with clinical observations. The aim of this study was to investigate whether a trajectory head movement task can differ between WAD patients, chronic non-traumatic neck pain (CNP) patients and asymptomatic controls. Study groups included subjects with WAD (n = 35) with persistent neck pain after a car accident, CNP (n = 45), and asymptomatic controls (n = 48). Head motion was recorded from an unsupported standing position using a 3D Fastrak device. A laser pointer was attached to the head and by moving the head the subjects were asked to trace a figure of eight displayed on the wall at three different paces (slow, moderate and fast). The motion signal was decomposed into 1 Hz frequency bands and angular velocity (deg/s) within each frequency band was calculated. Significantly higher angular RMS velocity was found in the WAD group compared to the two other groups for the slow paced test (3-4 and 4-5 Hz frequency bands) and the moderate paced test (3-4 Hz frequency band) indicating irregular and uncoordinated movements. Angular RMS velocity was associated with pain and dizziness, but only with severe symptom levels. In conclusion, irregular head movements during a complex task were found in the WAD group, indicating altered central sensorimotor processing. The irregularities were found within frequency levels observable to clinicians.