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Proton pump inhibitors (PPIs) are commonly prescribed to infants and children for managing gastroesophageal reflux disease (GERD). Recently published literature illustrates conflicting evidence on the efficacy of PPIs in infants and children. Randomized controlled trials and systematic reviews have demonstrated a lack of efficacy of PPIs, specifically in young infants. Furthermore, emerging evidence also suggests that PPIs are not as benign as once thought, with newer data implicating a potential association of PPIs with an increased risk of respiratory tract infections, gastrointestinal infections, bone fractures, hypomagnesemia, and the occurrence of rebound hyperacidity after discontinuation of PPI therapy. To summarize the emerging data in children, we reviewed the literature to assess the efficacy and safety of PPIs in managing pediatric GERD. Despite conflicting evidence on the efficacy of PPIs, most studies in children demonstrated some benefit when compared with placebo. With respect to the safety of PPIs in children, only a few small studies and case reports indicated a potential association of PPIs with an increased risk of respiratory tract or gastrointestinal infections, bone fractures, and hypomagnesemia; however, many of those studies had their own limitations. From the review, it is clear that further well-designed trials and observational studies are needed to shed more light on the efficacy and safety of PPIs in the pediatric population.