The basal ganglia act through direct and indirect striatopallidal output pathways that have different effects on cortical activity. This division has been proposed to underlie the fundamental distinction between hyperkinetic and hypokinetic movement disorders such as Parkinson's disease and Huntington's disease. Evidence to date does not favor a relationship between this dual organization and the division of the striatum into striosome and matrix compartments. However, the possibility has been raised that the division of striatopallidal output paths reflects a compartmentalization of the matrix itself into clusters of different striatopallidal projection neurons. We directly tested this hypothesis in squirrel monkeys by comparing the distributions of striatal output neurons retrogradely labeled from the two pallidal segments. Striatopallidal neurons labeled by small injections confined to either the external pallidum (GPe) or the internal pallidum (GPi) formed small clusters (“matrisomes”) in the matrix compartment of the putamen. However, contrary to previous predictions, labeled matrisomes projecting to GPe were not systematically separated from those projecting to GPi. They could overlap extensively, and within individual matrisomes GPe-projecting neurons and GPi-projecting neurons were extensively intermixed. Double- retrograde labeling analysis in single sections demonstrated that only 2.1 +/- 2.7% of labeled striatal neurons were doubly labeled from both GPe and GPi--a number not significantly different from zero. GPe- projecting and GPi-projecting neurons in the putamen also differed sharply in their expression of enkephalin-like immunoreactivity: 71.3 +/- 7.6% of the neurons labeled by GPe injections were enkephalin positive, in contrast to 10.0 +/- 3.6% of the neurons labeled by GPi injections. These results suggest that in the primate, populations of striatopallidal output neurons are grouped in clusters in the matrix, but that individual neurons in any given cluster project either to GPe or to GPi. Matrisomal clustering may thus coordinate signals sent into the direct and indirect pathways of the basal ganglia from distributed populations of projection neurons in the striatum.