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Beneficial therapeutic effect of probiotics has been reported in children with the irritable bowel syndrome (IBS) but not consistently in other functional abdominal pain-related disorders. The aim of the present study was to investigate the effect of Lactobacillus reuteri DSM 17938 in the treatment of functional abdominal pain (FAP) and IBS in children.Children (age 4–18 years) referred to pediatric gastroenterologist at Children's Hospital Zagreb from May 2012 to December 2014, diagnosed as FAP or IBS, were randomized to receive L reuteri DSM 17938 108 CFU daily or placebo. The study was a prospective, randomized, double-blind, placebo-controlled parallel study. Symptoms were evaluated using Wong-Baker FACES pain rating scale for pain and Bristol scale for stool shape and consistence.Data were analyzed for 55 children (26 in the intervention group and 29 in the placebo group). Children in the intervention group had significantly more days without pain (median 89.5 vs 51 days, P = 0.029). Abdominal pain was less severe in children taking probiotics during the second month (P < 0.05) and fourth month (P < 0.01). The 2 groups did not differ in the duration of abdominal pain, stool type, or absence from school. Both groups experienced significant reduction in the severity of abdominal pain from first to fourth month, with the reduction more prominent in the intervention group (P < 0.001 vs P = 0.004).Administration of L reuteri DSM 17938 was associated with a possible reduction of the intensity of pain and significantly more days without pain in children with FAP and IBS.