The mechanism of action of flunarizine (FZ) and cinnarizine (CZ) on the CNS is not fully understood. Computer analysis of saccadic eye movements (SEM) provides a sensitive and objective method for evaluating drug effect on the function of specific brain structures. This study aimed to assess the effect of a single oral dose of FZ (20 mg) and CZ (150 mg) on CNS function by means of computer analysis of SEM. Ten healthy volunteers were studied according to a double-blind, cross-over, placebo-controlled design. Peak saccadic velocity (PSV), which is related to the function of a specific group of burst neurons located in the brain stem, was significantly reduced by FZ. No significant effect of FZ on saccade accuracy (SA) and saccade latency (SL) was found. CZ did not produce significant effects on SEM, but a trend to decrease PSV. The possibility that a FZ central effect may be related to a stabilizing action on burst activity of neurons is discussed.