Oligonucleotide probes that recognize two cloned splice variants (5-HT4S and 5-HT4L) of 5-HT4 receptors were used to study by in situ hybridization the localization in rat brain of mRNA encoding these receptors. A probe common to both variants reveals high levels of transcripts in olfactory tubercle, some components of the basal ganglia (caudate putamen, ventral striatum), medial habenula and hippocampal formation. Similar patterns of distribution are obtained with probes that recognize each splice variant individually, suggesting that no dramatic differences exist in their respective regional distribution. Comparison of mRNA distribution with receptor distribution as visualized with [125I]SB 207710 indicates that 5-HT4 receptors are localized both somatodendritically in e.g. caudate putamen and on axon terminals in e.g. substantia nigra and globus pallidus.