Rabbits were trace-conditioned with a tone as a conditioned stimulus and an airpuff as an unconditioned stimulus. Electrical stimulation to the medial forebrain bundle in the lateral hypothalamus was delivered either before or after the tone-airpuff pair. The purpose of the present study was to test whether the effect of post-trial hypothalamic stimulation differed from the effect of pre-trial hypothalamic stimulation on trace conditioning in the same subjects. Additionally, hippocampal responses were measured during sessions to see if hypothalamic stimulation activated dopaminergic fibres and affected hippocampal cell functioning and thus learning. The results showed that behavioral nictitating membrane conditioned responses were acquired quickly and hippocampal multiple unit activity increased with post-trial hypothalamic stimulation in comparison to almost non-existent conditioned responses and activity changes in the pre-trial hypothalamic stimulation sessions. The results suggest that hypothalamic stimulation affects trace conditioning differently depending on its time of delivery during conditioning.