Schizophrenia is associated with subtle eye movement and brain structural abnormalities, but the extent to which these abnormalities occur in the same individuals is unclear. The relationship between quantitative measures of eye movement task performance (smooth pursuit and antisaccade) and MRI volumetric measurements (whole brain volume, prefrontal region, lateral ventricles, third ventricle, hippocampus, and cerebellum) was assessed in 70 patients with schizophrenia or schizoaffective disorder, 105 of their unaffected first-degree relatives and 68 controls. There was a lack of correlation between eye movement and morphometric abnormalities suggesting largely separable neurobiological pathways underlying the morphological and the eye movement deviations that have previously been identified in these patients. However, in the total sample, smaller prefrontal lobe volume was significantly associated with longer latency of correct antisaccades (partial correlation r = −0.22, p = 0.01) in line with previous studies demonstrating the importance of frontal lobe structures in performance of the antisaccade task. Also larger third ventricular volume was associated with larger mean amplitude of intrusive saccades during smooth pursuit (r = 0.28, p = 0.01). There were no significant between-group differences in the relationship between measures of eye movement and morphometry.