OBJECTIVE: The objective of this study was to investigate the effect of probiotics on functional abdominal pain disorders (FAPD) and functional constipation (FC). METHODS: A systematic review was conducted, searching PubMed and Cochrane databases from inception to January 2018 for randomized controlled trials (RCTs) investigating the efficacy of probiotics in children aged 4 to 18 years with FAPD or children aged 0 to 18 years with FC. RESULTS: A total of 657 citations were identified. Finally, 11 RCTs for FAPD and 6 RCTs for FC were included. Some evidence exists for Lactobacillus rhamnosus GG (n=3) in reducing frequency and intensity of abdominal pain in children with irritable bowel syndrome. There is no evidence to recommend L. reuteri DSM 17938 (n=5), a mix of Bifidobacterium infantis, Bifidobacterium breve and Bifidobacterium longum (n=1), Bifidobacterium lactis (n=1) or VSL#3 (n=1) for children with FAPD. No evidence exists to support the use of Lactobacillus casei rhamnosus LCR35 (n=1), B. lactis DN173 010 (n=1), B. longum (n=1), L. reuteri DSM 17938 (n=1), a mix of B. infantis, B. breve and B. longum (n=1), or Protexin mix (n=1) for children with FC. In general, studies had an unclear or high risk of bias. CONCLUSIONS: Insufficient evidence exists for the use of probiotics in FAPD and FC, only L. rhamnosus GG seems to reduce frequency and intensity of abdominal pain but only in children with irritable bowel syndrome. A better understanding of differences in gut microbiota in health and disease might lead to better probiotic strategies to treat disease.