To study the effects of low dose amitriptyline on cardiac conduction in children. Secondary analysis of data obtained from a double-blind, randomized placebo-controlled trial, evaluating low dose amitriptyline in children with a diagnosis of functional abdominal pain, functional dyspepsia, and irritable bowel syndrome according to the Rome II criteria. Children 8-17 years of age were recruited from the pediatric gastroenterology clinics of 6 tertiary care centers in the United States. The electrocardiograms (EKGs) done prior to initiation of amitrityline and 1 mo after initiation of amitriptyline were examined. The changes in cardiac conduction were evaluated in patients and controls. Thirty children were included in the study. There were 12 patients, ages 9-17 years of both genders, in the amitriptyline treatment group and 18 patients, ages 9-17 years of both genders, in the placebo treatment group. None of the patients had any baseline EKG abnormality. Amitriptyline use was associated with an increase in heart rate (P = 0.024) and QTc interval (P = 0.0107) as compared to pre-EKGs. Children in the placebo group were also noted to present a statistically significant increase in QTc interval (P = 0.0498). None of the patients developed borderline QTc prolongation or long-QT syndrome after they were started on amitriptyline. The study findings suggest that once patients with functional gastrointestinal disorders have been screened for prolonged QTc interval on baseline EKG, they probably do not need a second EKG for reevaluation of cardiac conduction after starting low dose amitriptyline.