High-resolution 3D reconstruction and morphometric analysis of striosomes was carried out in macaque monkeys by using immunocytochemistry for the Kv4 potassium channel subunit potassium channel interacting protein 1 (KChIP1), a novel marker. The striosomes form a connected reticulum made up of two distinct planar sheets spanning several millimeters in the putamen, and long finger-like branches in the caudate nucleus and putamen. Although their spatial organization is variable, morphometric analysis of the striosomes, utilizing skeletonizations, reveals several quantitative invariant measures of striosome organization, including the following findings: 1) individual bifurcation-free striosome branches are 355 +/- 108.5 microm in diameter and 1,013 +/- 751 microm in length, and are both lognormally distributed; and 2) striosome branches exhibit three pronounced orientation preferences that are approximately orthogonal. The former finding suggests a fundamental anatomical and functional component of the striatum, whereas the latter indicates that striosomes are more lattice-like than their spatial variability suggests. The perceived variable spatial organization of the striosomes in primates belies many invariant features that may reflect striatal function, development, and pathophysiology.