Background The association between Dientamoeba (D.) fragilis and the aetiology of functional gastrointestinal disorders (FGID) in children is unclear.

Aim The aim of this retrospective case–control study is to clarify the clinical relevance of D. fragilis in children with chronic abdominal pain.

Methods From April 2011 until April 2013, a total of 132 patients with chronic abdominal pain (AP), aged 8–18 years, referred to a non-academic hospital, and 77 control patients, aged 8–18 years without gastrointestinal symptoms referred to a psychiatric hospital, were included in the study. D. fragilis was diagnosed by real-time PCR in faecal samples. Symptomatic children without a D. fragilis infection fulfilled the ROME III criteria for AP-related FGID (AP-FGID). Clinical data were retrospectively analysed by examining patients’ hospital records from the Jeroen Bosch Hospital and Herlaarhof in The Netherlands.

Results D. fragilis was detected in 57 patients with chronic AP (43.2%) and in 39 controls (50.6%) (p=0.255). No significant differences in symptomatology were found between D. fragilis-infected children and children fulfilling the criteria for AP-FGID. Parasitological eradication was achieved in 61.7% of patients after treatment with metronidazole or clioquinol, while clinical improvement occurred in only 40.4% of patients (p=0.435).

Conclusions There were no differences in symptoms comparing children with and without D fragilis infection. Furthermore, no relation was found between clinical and microbiological response after treatment for D. fragilis. This retrospective study suggests that there is no association between chronic AP and D. fragilis infection.