The aim of this study was to investigate the effect of single-pulse transcranial magnetic stimulation on the triggering of saccades. The right frontal eye field was stimulated during modified gap and overlap paradigms with flashed presentation of the lateral visual target of 80 ms. In order to examine possible facilitating or inhibitory effects on saccade triggering, three different time intervals of stimulation were chosen, i.e. simultaneously with onset of the target, during the presentation and after target end. Stimulation applied simultaneously with target onset significantly decreased the latency of contralateral saccades in the gap but not in the overlap paradigm. Stimulation after target end significantly increased saccade latency for both sides in the gap paradigm and for the contralateral side in the overlap paradigm. Stimulation during presentation had no effect in either paradigm. The results show that, depending on the time interval and the paradigm tested, a facilitation or inhibition of saccade triggering can be achieved. The results are discussed in a context of two probable transcranial magnetic stimulation effects, a direct interference with the frontal eye field on the one hand and a remote interference with the superior colliculus on the other hand.