Basal ganglia (BG) are believed to involve in motor planning and control. Its striatum receives cortical, thalamic, and substantia nigra inputs and shows uneven distribution of μ-opioid receptor (MOR)-rich striosome and poor matrix. Medium spiny striatal neurons (MSN), distinguished into direct and indirect pathway, are present in both the striosome and matrix. Striatum also contains cholinergic and parvalbumin (PV) interneurons. Despite the complexity, BG are usually discussed with its direct and indirect pathways and overlooking the striosome and matrix compartmentation. Here we studied the relationship between inputs and striosome/matrix in rat striatum. Striosome/matrix are prominent in rostral and dorsal striatum. Primary somatosensory-cortical fibers terminated in a small dorsolateral patch while somatomoto-cortical fibers in a zone from the mid-lateral border to the striatum center. Association-cortical fibers prefer dorsal striatum while limbic-cortical fibers terminate more in ventromedial striatum. Thalamostriatal fibers terminated widely and usually outside the primary cortical input zone. All cortical and thalamic inputs terminated in the matrix exclusively. Nigrostriatal projection terminated profusely and more in the matrix as well. All the inputs appear to drive MSN dendritic spines and their cell bodies were surrounded by PV+ boutons. Cholinergic neuronal bodies stayed peripheral to the striosome. Thus, external inputs appear to activate and nigrostriatal and cholinergic fibers to modulate matrix MSNs first. This argues that the striatal striosome/matrix compartmentation shall be incorporated in the formulation of BG neuronal circuitry. This proposition is in accord with recent evidences that autistic spectrum disorder brain showed abnormal striosome and matrix morphology. (Supported by NSTC)