BACKGROUND: The use of complementary and alternative medicine (CAM) is becoming increasingly popular in Middle Eastern countries; it is often used for paediatric medical conditions such as chronic gastrointestinal complaints and failure to thrive. It is also commonly used in patients with chronic hepatic conditions such as cirrhosis and in hepatic transplant patients. AIMS: This study aimed to evaluate the prevalence, types and associated factors of CAM use in children with hepatogastrointestinal disease in Shiraz, Islamic Republic of Iran. METHODS: In a cross-sectional study carried out during September 2013-January 2014, 238 parents of children attending a paediatric gastroenterology and hepatology clinic at Shiraz University of Medical Sciences received a self-administered questionnaire covering associated factors of complementary and alternative medicine use; 210 questionnaires were completed and returned. RESULTS: Complementary and alternative medicine was used by 103 patients (49%); 74 (71.8%) of these used herbal remedies. Older age of the child significantly increased CAM use. Those with previous positive experience of CAM (62.1% of users, 40.2% of non-users) and those who had received recommendation for CAM by health care providers (24.3% of users, 6.6% of non-users) were significantly more likely to use CAM. CONCLUSIONS: This survey demonstrated the high prevalence of CAM use (especially herbal remedies) in paediatric patients with hepatogastrointestinal diseases.