The ultrastructural localization of putative excitatory (glutamate, aspartate) and inhibitory (taurine, glycine) amino acid neurotransmitters is described in several selected rat brain regions. In general, axon terminal profiles immunoreactive for excitatory amino acids formed asymmetric synapses with non-immunoreactive small diameter dendritic profiles or dendritic spines. In the cerebellum, both mossy fiber terminals and parallel fiber terminals were immunoreactive for glutamate and aspartate. In the hippocampus, mossy fiber terminals within the stratum lucidum of the CA3 region were immunoreactive for glutamate. Localization of glutamate and aspartate to cerebellar parallel and mossy fibers, as well as the identification of glutamate in hippocampal mossy fibers, is consistent with the excitatory nature of these fibers as described in previous physiological studies. Glutamate-like immunoreactive terminals were also identified in subnucleus caudalis of the spinal trigeminal nucleus and in the dorsal horn of the spinal cord. Immunoreactive axon terminals for two putative inhibitory neurotransmitters, glycine and taurine, displayed a greater number of morphological variations in synaptic structure. In the cerebellum, taurine-like immunoreactivity was present in both basket cell axon terminals which formed symmetric synapses with Purkinje cell neurons, and in a few mossy fiber terminals which formed asymmetric synapses with dendritic spines. In the area dentata of the hippocampus, taurine-like immunoreactive profiles formed asymmetric synapses with dendritic elements. Glycine-like immunoreactive terminals formed symmetric synapses with cell perikarya in both the ventral horn of the spinal cord and in the cochlear nuclei, and on axon terminals in the spinal trigeminal and cochlear nuclei. In contrast, some glycine-like immunoreactive terminals formed asymmetric synapses with distal dendritic profiles in the spinal cord and spinal trigeminal nucleus. The localization of taurine to cerebellar basket cell axons and glycine to axon terminals that synapse on ventral horn motor neuron perikarya is consistent with the hypothesis that these amino acids are functioning as inhibitory neurotransmitters at these synapses. Taurine localization to cerebellar mossy fibers and to fibers in the molecular layer of the dentate gyrus may be more consistent with a proposed neuromodulator role of taurine.