The aim of this study was to evaluate the prevalence of functional gastrointestinal disorders (FGIDs) in children with migraine headache and the effects of flunarizine on gastrointestinal manifestations. We studied 50 migrainous children (mean age 8.63 years). The clinical pattern and the diagnosis of FGIDs were obtained from structured questionnaires. All subjects underwent measurement of total gastric emptying time (TGEt) performed by real-time ultrasonography of the gastric antrum at baseline (T0). In the second part of the study, we evaluated 10 migrainous children (mean age 9.8 years) with associated FGIDs. In these 10 patients, repeated TGEt evaluation together with a detailed symptom history was obtained after 1 (T1) and 2 months (T2) of treatment with flunarizine. Control groups were composed of 10 migrainous children without FGIDs (mean age 9.2 years) and nine sex- and age-matched healthy children. Gastrointestinal disorders were present in 70% of the patients. Migrainous children with FGIDs had significantly (P < 0.01) more prolonged TGEt than subjects without FGIDs. Prior to therapy, all migrainous children with FGIDs had prolongation of TGEt compared with controls (P < 0.05). Patients on flunarizine had a significant decrease in TGEt at both 1 (P < 0.01) and 2 months (P = 0.002) of therapy. The mean frequency of abdominal pain per month was significantly (P < 0.001) reduced at T1 compared with T0. The mean frequency of vomiting per month was significantly decreased at T1 (P < 0.05) and even more so at T2 (P < 0.01). Finally, the mean frequency of headache per month was significantly reduced only at T2 (P < 0.05), whereas the mean duration of headache was significantly decreased at T1 (P < 0.01) with no difference between T1 and T2. Most children with migraine report FGIDs, associated with a delayed gastric emptying. Flunarizine decreases the frequency and duration of migrainous episodes as well as the gastrointestinal symptoms.