The diagnosis of Hirschsprung’s disease relies on histologically proven aganglionosis and nerve trunk hypertrophy in rectal biopsies. Although the frequency of inconclusive biopsies is relatively low, it is a relevant clinical problem. The aim of the present study was to investigate whether a re-evaluation of archived full-thickness biopsies (FTBs) stained with hematoxylin and eosin (HE), together with immune histochemical (IHC) staining, would be diagnostic in biopsies otherwise deemed inconclusive at initial examination with HE only. A total of 34 inconclusive biopsies in 31 patients were identified. From each tissue block, three slices were cut and stained with HE, S100 and calretinin. A blinded pathologist examined the tissue samples. At re-evaluation, one patient was found positive for HD and 11 negative for HD with both HE and IHC staining, respectively. In all 12 cases, the result was confirmed by the final diagnosis at a 5-year follow-up. The rest of the cases were deemed inconclusive. A re-evaluation of the remaining tissue from the biobank might have saved one third of the children from a re-biopsy. The value of adding IHC to conventional HE staining is dubious.