A new rabbit polyclonal antiserum against choline acetyltransferase (ChAT) reveals that cholinergic innervation of the cortex varies strikingly among different cytoarchitecturally defined areas in the rat neocortex. These findings suggest that cholinergic transmission may be integrated differently into the local circuitries of various regions of the cerebral cortex. In addition, the pattern of staining observed with acetylcholinesterase histochemistry, which has been used for many years to demonstrate putative cholinergic fibers, only partially matches the staining pattern obtained with the more specific cholinergic marker, ChAT.