Cyclical vomiting syndrome (CVS), and abdominal migraine (AM) are relatively unusual periodic syndromes, generally believed to be migraine equivalents, and are characterized by recurrent and severe paroxysmal episodes of vomiting and/or abdominal pain lasting hours to days, separated by weeks to months of no symptoms. Flunarizine is a calcium channel-blocking agent that has been used successfully as a prophylactic agent in the prevention of both childhood and adult-onset migraine syndromes. The purpose of this study was to evaluate the efficacy of flunarizine as a prophylactic/preventive agent in the treatment of CVS and AM. Eight children with CVS and 10 children with AM were included in the study. The mean dose of flunarizine was 5 mg/day in children with CVS, and 7.5 mg/day in children with AM. Follow-up ranged from 6 to 24 months (mean 13 months). There was a 57% reduction in frequency and 44% reduction in duration of attacks of CVS, and a 61% reduction in frequency and 51% reduction in duration of attacks of AM. Sixty-four percent of patients with CVS and AM had history of episodic recurrent headaches with 60% reduction in frequency of attacks on treatment. Flunarizine showed to be equally efficacious than previously tried therapies in the prophylaxis of a small cohort of patients with CVS and AM.