A marked histochemical compartmentalization is visible in the substantia nigra of the squirrel monkey in sections stained for acetylcholinesterase (AChE). In nigral regions containing tyrosine hydroxylase-positive neurons, there are AChE-poor and AChE-rich zones, and many of the AChE-poor zones have the form of narrow fingers extending ventrally into an AChE-rich matrix (Jimenez-Castellanos and Graybiel 1987b). The study reported here was carried out to determine whether this histochemical heterogeneity of the primate's substantia nigra is related to the known differentiation within its pars compacta of subdivisions projecting respectively to the caudate nucleus and to the putamen. Retrograde and anterograde labeling in the substantia nigra was elicited by tracer injections placed in the caudate nucleus or putamen and was plotted in relation to patterns of AChE staining and tyrosine hydroxylase immunostaining. Much of the labeling observed was organized according to borders visible with AChE histochemistry: labeled nigral neurons (and afferent fibers) tended to be clustered precisely within the AChE-poor ventrally-extending fingers or to be situated outside these zones. However, projection neurons in these ventrally-extending fingers were not exclusively related either to the caudate nucleus or to the putamen. After injections in the caudate nucleus, labeled neurons were predominantly in the AChE-poor fingers in some cases, but predominantly in AChE-rich nigral zones outside them in other cases. Labeling in and out of the ventrally-extending fingers, and along the edges of the fingers, also occurred following different tracer injections in the putamen. These findings confirm the independent clustering of nigrostriatal neurons projecting respectively to the caudate nucleus and to the putamen. The plan of nigrostriatal connections additionally appears concordant with the histochemical compartmentalization of the substantia nigra that can be detected with acetylthiocholinesterase histochemistry.