In the central nervous system small conductance Ca2+-activated K+ (SK) channels are important for generating the medium/slow afterhyperpolarization seen after single or trains of action potentials. Three SK channel isoforms (SK1,-2,-3) are differentially distributed throughout the brain, but little is known about their specific expression in particular neuronal compartments. In the hippocampus SK3 was found in the neuropil, predominantly in the terminal field of the mossy fibres and in fine varicose fibres, but excluded from the pyramidal and granule cell layers. Because this expression pattern suggested a presynaptic localization, we examined the subcellular distribution of SK3 in cultured hippocampal neurons using high-resolution immunofluorescence analysis. SK3 was localized in a punctate, synaptic pattern. The SK3 clusters were precisely colocalized with the presynaptic marker synapsin and at close range (0.4-0.5 microm) from NMDA-receptors and PSD-95. This arrangement is consistent with a localization of SK3 in the presynaptic nerve terminal, but not restricted to the synaptic membrane proper. In agreement with the increasing expression of SK3 during early postnatal development in vivo, the fraction of synapses containing SK3 increased from 14% to 57% over a six-week culture period. SK3-containing synapses were equally observed on spiny, glutamatergic and smooth GABAergic neurons. In contrast to its close association with NMDA-receptors and PSD-95, SK3 was rarely associated with GABAA-receptor clusters. Thus, SK3 is a presynaptic channel in excitatory hippocampal synapses, with no preference for glutamatergic or GABAergic postsynaptic neurons, and is probably involved in regulating neurotransmitter release.