Conjugate eye deviation describes the tonic horizontal deviation of the eyes in acute stroke patients. Here we investigate whether measuring patients' eye-in-head position in clinical magnetic resonance imaging or computed tomography scans obtained at admission shows a specific relationship to spatial neglect. We investigated 124 continuously admitted subjects with unilateral, first-ever left- or right-sided stroke. To control for the possibility that the degree of eye deviation is related to lesion size rather than spatial neglect, overall lesion volume was used as a covariate in the statistical analysis. Horizontal eye-in-head deviation on clinical brain scans appeared to be associated with spatial neglect rather than with brain damage per se. In contrast to the subject groups without the disorder, the patients with spatial neglect showed an eye-in-head position that was significantly deviated towards the ipsilesional right. Evaluation of eye-in-head position on clinical scans thus may be an additional helpful tool for diagnosing spatial neglect, particularly in the very early period of the stroke.