The aim of the study was a comparative analysis of patients with chronic constipation and coexisting food allergy in relation to patients with functional chronic constipation without food allergy. 325 children with chronic constipation aged 0.6-17.1 years (mean 8.0 +/- 4.3) were included into the study. The IgE-mediated food allergy was diagnosed in 179 children. Results of anthropometric measurements, rectoscopies, abdominal ultrasonographies, evaluations of colonic transit time and anorectal manometric examinations, together with clinical symptoms, were analysed and compared. The results were subjected to statistical analysis. There were no significant differences in clinical presentation, anthropometric measurements, rectoscopic, ultrasonographic, manometric and histopathological findings between both groups. In the food allergy group the total and segmental colonic transit time more frequently was prolonged, manifested usually as colonic inertia (p < 0.001). Food allergy can be clinically manifested as a chronic constipation. IgE-mediated food allergy may significantly prolong colonic transit in affected patients.