Interstitial cells of Cajal (ICC) provide important regulatory functions in the motor activity of the gastrointestinal tract. In the small intestine, ICC in the myenteric region (ICC-MY), between the circular and longitudinal muscle layers, generate and propagate electrical slow waves. Another population of ICC lies in the plane of the deep muscular plexus (ICC-DMP), and these cells are closely associated with varicose nerve terminals of enteric motor neurons. Here we tested the hypothesis that ICC-DMP mediate excitatory and inhibitory neural inputs in the small bowel. ICC-DMP develop largely after birth. ICC-DMP, with receptor tyrosine kinase Kit-like immunoreactivity, appear first in the jejunum and then in the ileum. We performed electrophysiological experiments on mice immediately after birth (P0) or at 10 days post partum (P10) to determine whether neural responses follow development of ICC-DMP. At P0, slow-wave activity was present in the jejunum, but neural responses were poorly developed. By P10, after ICC-DMP developed, both cholinergic excitatory and nitrergic inhibitory neural responses were intact. Muscles of P0 mice were also put into organotypic cultures and treated with a neutralizing Kit antibody. Neural responses developed in culture within 3-6 days in control muscles, but blocking Kit caused loss of ICC and loss of cholinergic and nitrergic neural responses. Non-cholinergic excitatory responses remained after loss of ICC-DMP. Our observations are consistent with the idea that cholinergic and nitrergic motor neural inputs are mediated, to a large extent, via ICC-DMP. Thus, ICC-DMP appear to serve a function in the small intestine that is similar to the role of the intramuscular ICC in the stomach.