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Gold standard in Hirschsprung disease (HD) diagnosis is rectal suction biopsy (RSB) with hematoxylin and eosin and acetylcholinesterase (ACE) stainings. Sensitivity is 83–93 % and specificity is between 95 and 99 %. The rate of non-conclusive results (NC) due to inadequate samples or variability in the interpretation is about 11–37.8 %. Interpretation is still difficult in neonates. Calretinin (C) is a calcium-binding protein, expressed in the nervous system. It has been introduced as a marker to improve the diagnosis accuracy in HD. We compare sensitivity, specificity between ACE and ACE + C and investigate whether the introduction of C could reduce the rate of inconclusive results. We also tried to define the most adequate age to obtain accurate results from RSB. Data from patients undergoing rectal suction biopsies from 2005 to 2014 was analyzed. Until 2010 we used ACE; since 2011 we used ACE + C. The ROC curve analysis of the NC results regarding the age, showed an optimal cut-off point at 1.5 months (m). It divides the sample into two groups which we compared. We analyzed 91 patients. Results of the RSB: 40 HD (44 %), 34 no Hirschsprung (37.4 %) and 17 NC (18.7 %). Sensitivity = 97.5 %, specificity = 97.1 %, not including the NC (1 false positive, 1 false negative). Results depending on the staining: Results depending on the age: Calretinin decreases the rate of inconclusive results, but not significantly. The percentage of inconclusive results decreases in patients olders than 1.5 m. Further studies are necessary to determine if this technique is useful to improve RSB results in infants younger than 1.5 months.