Hirschsprung disease (HD) is reported in patients with Down syndrome with a frequency between 2% and 10%. The incidence of HD is 2% in our community-based registry that contains >700 patients with Down syndrome. We reviewed rectal biopsy findings in 32 of these patients who had suction rectal biopsy performed between 1980 and 2009 to investigate the cause of chronic constipation. We confirmed that 15 patients had diagnostic histologic and histochemical features of HD. More challenging were findings in 5 of 17 patients, in whom ganglia coexisted with equivocal acetylcholinesterase reaction patterns and/or hypertrophic submucosal nerves. In this retrospective study, we were able to resolve most of these discrepant findings by demonstrating normal calretinin-positive nerve twigs in the lamina propria and muscularis mucosae. The clinical significance of these unexpected findings in suction rectal biopsy specimens that did not satisfy strict criteria for a tissue diagnosis of HD is unknown. We speculate that a minority of these patients have transition zone morphology or an incomplete/atypical form of HD. Further investigations may help resolve discrepancies that arise when suction rectal biopsy is used to investigate chronic constipation in Down syndrome.