Current diagnostics in Hirschsprung’s disease are often challenging and invasive. This study aims to investigate whether surface electroenterography can non-invasively discern healthy subjects from subjects suffering from Hirschsprung’s disease. Nine healthy subjects (seven children, two adults) and eleven subjects suffering from surgically untreated Hirschsprung’s disease (nine children, two adults) underwent an electroenterography procedure. This procedure consisted of ultrasound-guided placement of surface electrodes on the abdomen covering all parts of the colon, fasting and two 20-min electroenterography measurements separated by a meal. The dominant frequency, magnitude and relative increase (pre- to postprandial) of colonic activity were compared between both groups. The results showed that in the pediatric group, no significant differences in dominant frequency, colonic activity and relative power increase were observed between controls and patients. The adult patients showed decreased colonic motility and relative power increase in the electrodes closest to the distal colon, both when compared to the same electrodes in controls and to the more proximal electrodes of themselves. To conclude, electroenterography measurements in young children is challenging, but the results in adults demonstrate that these measurements can possibly distinguish between controls and Hirschsprung’s patients. Therefore, optimization of electroenterography measurements in young children is necessary.