The distribution of cholinergic fibers in rat cortex was investigated using choline acetyl-transferase immunohistochemistry. Previous studies have either shown differences in distribution, but have been limited to selected areas, or have shown no discernable differences between different cortical areas. In our study, we examined all areas of rat cortex and found that there are striking interareal and interlaminar differences in cholinergic fiber distribution. We have found that certain functionally similar cortical areas (e.g. sensory, motor, etc.) have similar patterns of cholinergic innervation and we have designated 13 general patterns of cortical cholinergic innervation. We have also compared, on an area-by-area basis, the pattern of acetylcholinesterase reactivity to that of choline acetyltransferase immunoreactivity, since acetylcholinesterase has been used for many years as a putative cholinergic marker. We found that in most cortical areas, the distribution of acetylcholinesterase-positive fibers paralleled that of choline acetyltransferase-immunoreactive fibers; however, there were some striking differences, notably primary somatosensory (the "barrelfield"), retrosplenial and cingulate cortices. In some areas, a revised concept of rat cortical organization, using cytoarchitectonics, was required. The results of this study provide a comprehensive microscopic analysis of cholinergic fiber innervation of the rat cortex. These results are discussed in relation to previous anatomical, physiological and pharmacological studies of cortical cholinergic innervation. The possible sources of this innervation are also discussed.