The neurotransmitter-synthesizing enzymes choline acetyltransferase and glutamate decarboxylase were localized immunocytochemically at the light microscopic level. Their respective laminar distributions were compared in 17 different cytoarchitectural areas, comprising limbic and neocortical regions of rat cerebral cortex. The immunoreactive intensities within these areas were measured with an image analysis system and dark-field optics. Choline acetyltransferase and glutamate decarboxylase immunoreactivity displayed distinctive distribution patterns throughout the cerebrum. In general, limbic cortex showed greater intensity of both choline acetyltransferase and glutamate decarboxylase immunoreactivity than neocortex. For example, choline acetyltransferase immunoreactivity in pyriform and retrosplenial cortex was 54% and 29% greater, respectively, than in neocortex, and glutamate decarboxylase immunoreactivity in the same cortical areas was 5% and 17% greater, respectively. In addition to these regional differences, the marked variations of choline acetyltransferase and glutamate decarboxylase immunostaining were characterized as either coincidental or complementary when comparing their laminar distributions. The laminar pattern and relative intensities of choline acetyltransferase and glutamate decarboxylase immunostaining were coincident in some layers of all cortical regions. For example, both choline acetyltransferase and glutamate decarboxylase immunoreactive intensities were high in cellular layers II and IV of the entorhinal cortex. In contrast, examples of complementary choline acetyltransferase and glutamate decarboxylase immunoreactive patterns were observed in retrosplenial cortex and neocortex. In neocortex, layers III and part of V were intensely glutamate decarboxylase-positive, whereas these same layers were less intensely choline acetyltransferase immunoreactive than the intervening layer IV and upper part of V. Quantitatively, choline acetyltransferase immunoreactivity in layers IV and upper V was 27-37% greater than adjacent layers II and deep V. The glutamate decarboxylase immunostaining pattern was complementary in that layer IV was 19-23% less intensely stained than adjacent layers III and V. Our results demonstrate that terminals immunoreactive for choline acetyltransferase and glutamate decarboxylase, and presumably the synaptic terminals that respectively use acetylcholine or gamma-aminobutyric acid as their neurotransmitters, are distributed in distinct laminar patterns that are strategically situated for modulating either afferent information in the case of cholinergic terminals or efferent transmission for GABAergic endings.(ABSTRACT TRUNCATED AT 400 WORDS)