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The neostriatum has a mosaic organization consisting of striosome and matrix compartments. It receives glutamatergic excitatory afferents from the cerebral cortex and thalamus. Recent behavioral studies in rats revealed a selectively active medial prefronto-striosomal circuit during cost-benefit decision-making. However, clarifying the input/output organization of striatal compartments has been difficult because of its complex structure. We recently demonstrated that the source of thalamostriatal projections are highly organized in striatal compartments. This finding indicated that the functional properties of striatal compartments are influenced by their cortical and thalamic afferents, presumably with different time latencies. In addition, these afferents likely support the unique dynamics of striosome and matrix compartments. In this manuscript, we review the anatomy of basal ganglia networks with regard to striosome/matrix structure. We place specific focus on thalamostriatal projections at the population and single neuron level.Thalamic projections primarily arise from the intralaminar and midline thalamic nuclei.Thalamostriatal projections project predominantly to the striatal matrix compartment.Ultrastructural images revealed that 84% of thalamostriatal projections synapsed on dendritic spines in striosomes, whereas 70% synapsed on dendritic shafts in the matrix compartment.Single thalamic neurons in the midline nuclei projected to the striatal striosome compartment and to the limbic cortex.