Experiments were performed to test the hypothesis that there is a characteristic distribution of neuronal c-fos expression associated with the classical conditioning of the rabbit nictitating membrane reflex (NMR). Rabbits were divided into two groups: a conditioning group that received paired tone and airpuff stimuli in a traditional delay NMR conditioning paradigm and a pseudo-conditioning group in which the same number of tone and airpuff stimuli were applied but without being paired. Labeling was present in similar brainstem nuclei in both groups of animals. The labeled sites included trigeminal and auditory nuclei in the classical pathway for the nictitating membrane reflex as well as other nuclei such as the raphe nuclei and those in the ventrolateral medulla (VLM). However, there were quantitative differences in the labeling between the two groups. There were significantly more labeled nuclear profiles in the trigeminal nucleus of the pseudoconditioned rabbits, but more labeled nuclear profiles in the raphe nuclei in the conditioned animals. Interestingly, the ratio of the labeling in the raphe versus the VLM strongly differed between the two groups.