Protein gene product (PGP) 9.5 is a newly characterized brain-specific protein originally detected by high-resolution two-dimensional electrophoresis of soluble human brain proteins. Immunoreactivity for PGP9.5 was investigated in the small and large intestine of aganglionic mutant and control rats with light microscopy, electron microscopy, and confocal laser scanning microscopy. Immunoreactive spindle-shaped cells were seen in the inner circular muscle layer of the aganglionic ileal segment. The long axes of these spindle cells paralleled the inner circular muscle fibers. PGP9.5-positive spindle cells were positive for enteric actin, and some of them were also positive for vimentin, a relatively specific marker for the special smooth muscle (pacemaker cells). These cells may prove to be a maldeveloped microenvironment of aganglionic segment. However, it is necessary to investigate expression of PGP9.5 in embryonal tissue with an abnormal environment to test this hypothesis. This study showed PGP9.5-positive pacemaker cells in the aganglionic ileal segment in the first time.