Gastro-oesophageal reflux (GOR) disease is very common and, in the majority of infants, is physiological. However, untreated GOR disease in infants and children is associated with a decrease in quality of life for the child and their parents. It may also cause sometimes more severe complications, such as oesophagitis, and causing, in rare cases, failure to thrive, oesophageal stricture, apnoea and even death. Every therapeutic intervention (non-drug treatment, medical treatment and surgery) is associated with morbidity and even mortality. Moreover, efficacy data of many medications in children are non-existing, limited or disappointing. The safety profile of cisapride is comparable to that of other therapeutic interventions or to the risk of non-treatment. Therefore, the therapeutic approach of GOR disease in infants and children needs to be well-balanced, considering therapeutic efficacy and side effects. This review will focus on the side effects of the different therapeutic options.