Evaluation of rectal biopsies for ganglion cells is performed for patients suspected of having Hirschsprung disease. At times, identification of ganglion cells can be difficult, especially in newborns. To assist in diagnosis, frozen tissue can be collected for acetylcholinesterase histochemical staining. At our institution, we developed a protocol using peripherin and S-100 immunostaining as an adjunct to hematoxylin and eosin (H&E) for the identification of ganglion cells. Further, at the time of frozen section, we performed Diff Quik staining to highlight ganglion cells. One hundred and thirty eight rectal biopsies submitted for evaluation of Hirschsprung disease were compiled from the archives of the Medical College of Georgia from 2002 to 2009. Initial evaluation consisted of eight levels of H&E-stained slides and two unstained slides each for immunostaining with peripherin and S-100. If on initial evaluation, ganglion cells were not identified, additional H&E and peripherin immunostains were performed. Peripherin immunostaining was unequivocally identified in the cytoplasm of ganglion cells of patients at all ages. Of the 136 patients with diagnostic biopsies, 80% had ganglion cells. Of these, 93% of cases were diagnosed on the original eight levels. Twenty-seven cases were devoid of ganglion cells, and of these, 81% showed submucosal neural hypertrophy on S-100 staining. Twenty-six patients had confirmed aganglionic segments at the time of colonic resection. One patient had colostomy only. A total of 54 frozen sections were performed on 25 patients over this same period of time. Diff Quick staining was found to be very useful. In this study, our protocol proved to be very sensitive, specific, and efficient for the diagnosis of Hirschsprung disease.