The striatum is anatomically organized into both distinctly bounded compartments (striosomes) and gradients of neuronal markers. Biochemical markers of striatal cholinergic systems are distributed in increasing amounts laterally. We have investigated the morphologic basis of this gradient by quantitative analysis of neuronal somata and neuropil stained immunocytochemically for choline acetyltransferase (ChAT). We found in both immature and adult rats that there was no difference in the density (neurons mm2) of somata in the medial and lateral compartments. In both age groups, however, there was a clear increase in ChAT-positive neuropil laterally. This medial to lateral gradient was present in all striatal planes examined. This gradient corresponds to the distribution of some other, non-cholinergic, striatal biochemical markers, and is likely to represent an important organizational feature of striatal anatomy, with functional implications.