Little is known about the alterations in the neurochemical anatomy of the brain in the static encephalopathies of childhood, of which one cause is hypoxia-ischemia. We and others have previously shown in neonatal rodent that experimental hypoxia-ischemia results in an increase in the density of striatal cholinergic neurons (number/mm3). There is a rostrocaudal gradient for this effect within the striatum, with as much as a 50% increase in density caudally. It has not been known what effect this injury has on the distribution of striatal cholinergic neuropil. We have therefore investigated effects on striatal cholinergic neuropil, demonstrated with a monoclonal antibody to choline acetyltransferase (CAT) and the immunoperoxidase technique. Because individual CAT-positive fibers in the striatum are too numerous to be directly counted, we have quantified relative effects on neuropil at the population level using segmented field analysis within the same section. We find that hypoxic-ischemic injury results in a significant increase in the proportion of the injured striatum occupied by high density CAT-positive neuropil staining. This change is persistent, as it is also observed in adult rats. The increase is uniform in the rostrocaudal dimension. Our measure of CAT-positive neuropil staining, being relative, cannot determine whether the observed increase in staining is strictly due to striatal shrinkage with compaction of fibers or whether, in addition, there has been sprouting. The latter possibility is suggested by the lack of a correlation between the degree of shrinkage and changes in area occupied by positive staining. While the functional significance of these changes is not known, they support the concept that striatal cholinergic systems are resistant to hypoxic-ischemic injury and that an abnormal predominance of these systems may play a role in the persistent alterations of motor control observed clinically in this form of injury.