The organization of the magnocellular basal nucleus (MBN) projection to cerebral cortex in the rat has been studied by using cytoarchitectonic, immunohistochemical, and retrograde and anterograde transport methods. The distribution of retrogradely labeled basal forebrain neurons after cortical injections of wheat germ agglutinin-horseradish peroxidase conjugate was essentially identical to that of neurons staining immunohistochemically for choline acetyltransferase. These large (20-30 micrometers perikaryon diameter) multipolar neurons were found scattered through a number of basal forebrain cell groups: medial septal nucleus, nucleus of the diagonal band of Broca, magnocellular preoptic nucleus, substantia innominata, and globus pallidus. This peculiar distribution mimics the locations of pathways by which descending cortical fibers enter the diencephalon. Each cortical area was innervated by a characteristic subset of MBN neurons, always located in close association with descending cortical fibers. In many instances anterogradely labeled descending cortical fibers appeared to ramify into diffuse terminal fields among MBN neurons which were retrogradely labeled by the same cortical injection. Double label experiments using retrograde transport of fluorescent dyes confirmed that MBN neurons innervate restricted cortical fields. Anterograde autoradiographic transport studies after injections of 3H-amino acids into MBN revealed that MBN axons reach cerebral cortex primarily via two pathways: (1) The medial pathway, arising from the medial septal nucleus, nucleus of the diagonal band, and medial substantia innominata and globus pallidus MBN neurons, curves dorsally rostral to the diagonal band nucleus, up to the genu of the corpus callosum. Most of the fibers either directly enter medial frontal cortex or turn back over the genu of the corpus callosum into the superficial medial cingulate bundle. Many of these fibers enter anterior cigulate or retrosplenial cortex, but some can be traced back to the splenium of the corpus callosum, where a few enter visual cortex but most turn ventrally and sweep into the hippocampal formation. Here they are joined by other fibers which, at the genu of the corpus callosum, remain ventrally located and run caudally through the dorsal fornix into the hippocampus. (2) The lateral pathway arises in part from medial septal, diagonal band, and magnocellular preoptic neurons whose axons sweep laterally through the substantia innominata to innervate primarily piriform, perirhinal, and endorhinal cortex. Some of these fibers may also enter the hippocampal formation from the entorhinal cortex via the ventral subiculum.(ABSTRACT TRUNCATED AT 400 WORDS)