Acetylcholine and dopamine afferents reach their cortical targets during periods of synaptogenesis, and are in position to influence the cytoarchitectural development of cortical neurons. To determine the effect of removing these afferents on dendritic development, we lesioned rat pups at 7 days of age with the selective immunotoxins 192 IgG-saporin, or 6-hydroxydopamine, or both. One group of rats was killed in adulthood for neurochemistry and another was prepared for morphology using Golgi-Cox staining. Changes in morphology were compared in layer V pyramidal cells from medial prefrontal cortex, which sustained the greatest dopamine depletion, and in layer II/III pyramidal cells from retrosplenial cortex, which sustained the greatest choline acetyltransferase depletion. In rats with acetylcholine lesions, layer V medial prefrontal cells had smaller apical tufts and fewer basilar dendritic branches. Both apical and basilar spine density was substantially reduced. Layer II/III retrosplenial cells also had smaller apical tufts and substantially smaller basilar dendritic trees. Apical and basilar spine density did not change. In rats with dopamine lesions, layer V medial prefrontal cells had fewer oblique apical dendrites and atrophied basilar trees. Layer II/III retrosplenial cells had fewer apical dendritic branches. In neither area were spine densities significantly different from control. Neurons from rats with combined lesions were always smaller and less complex than those from singly lesioned rats. However, these cells were simple, additive composites of the morphology produced by single lesions. These data demonstrate that ascending acetylcholine and dopamine afferents play a vital role in the development of cortical cytoarchitecture.