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Diagnosis of Hirschsprung disease (HSCR) relies on histologic and/or histochemical staining of sections from suction rectal biopsies. Acetylcholinesterase histochemistry (AChE) facilitates diagnosis but is not universally employed, in part because it requires special tissue handling. Calretinin immunohistochemistry (IHC) may be a useful alternative, because loss of calretinin immunoreactive nerves reportedly correlates spatially with aganglionosis. We investigated the patterns of calretinin IHC in suction rectal biopsies from HSCR and non-HSCR patients and compared the diagnostic value of calretinin IHC with a widely used rapid AChE method. In suction rectal biopsies that contain ganglion cells, small nerves in the lamina propria, muscularis mucosae, and superficial submucosa contain granular aggregates of calretinin immunoreactivity. Immunolabeling of these nerves is completely absent in the aganglionic biopsies of HSCR patients. Multiple observers independently reviewed calretinin IHC and AChE sections of suction rectal biopsies from 14 HSCR patients and 17 non-HSCR controls. Five observers, blinded to the correct diagnosis, scored each patient's calretinin IHC and AChE slides as HSCR, not HSCR, or equivocal. The frequencies of major and minor discrepant diagnoses were compared. Calretinin IHC yielded no misdiagnoses or major discrepancies between observers. In contrast, 2 misdiagnoses and significantly more interobserver disagreement resulted from the AChE-stained sections. Calretinin IHC appears to be a reasonable, and potentially superior, alternative to AChE as an adjunctive diagnostic method for evaluating suction rectal biopsies for HSCR.