Background: Despite their high incidence, costs, and long lasting disability, whiplash associated disorders (WAD) lack an identifiable objective pathology that explains their acute or chronic symptoms. Objective: In view of previous suggestions of a possible effect of neck torsion on several electro-oculography (EOG) parameters, the main objective of this study was to examine their applicability in differentiating patients from uninvolved subjects. Methods: Smooth pursuit and saccadic eye movements were assessed in 26 patients with chronic WAD and 23 healthy subjects. All tests were executed in three neck positions: neutral and rotations to left and right. Results: Neck torsion did not influence eye movement performance of either the WAD or healthy groups. However, compared with the healthy group, patients with WAD had significantly lower smooth pursuit velocity gain (SPVG) (p = 0.01) and prolonged saccadic latency (p = 0.001), irrespective of neck position. Conclusions: Despite scattered differences that reached significance, the electro-oculographic measures used in this study do not seem to offer a clinically relevant method for differentiating between patients with WAD and normal subjects.