Abdominal-pain related functional gastrointestinal disorders (FGIDs) are a frequent problem in a pediatric age group. Reported prevalence of chronic abdominal pain in children is 0.3% to 19%. In a great majority of children (>90%) pain has no identifiable organic cause and is considered to be of functional origin. FGIDs are defined by chronic or recurrent symptoms in the absence of structural or biochemical abnormalities. Two frequent categories of abdominal pain–related FGIDs in children are functional abdominal pain (FAP) and irritable bowel syndrome (IBS). FAP is defined as episodic or continuous abdominal pain occurring at least once per week for at least 2 months, with no evidence of inflammatory, anatomic, metabolic, or neoplastic process. Also IBS is defined as abdominal pain or discomfort associated frequently with relief after defecation, change in stool frequency, and/or a change in stool consistence. Pathogenesis of FAP and IBS remains unresolved; visceral hypersensitivity, motility disorder, psychosocial factors, and intestinal dysbiosis with the low-grade inflammation have all been implicated. Although the pathogenesis of abdominal pain-related FGIDs remains to be elucidated, changes in the intestinal flora and a persistent low-grade inflammation could be important determinants. Patients with IBS have a different composition of intestinal microbiome compared with healthy controls: decrease in the Bifidobacterium spp population, increased ratio of Firmicutes to Bacteroidetes, and reduction in Lactobacillus species have all been shown. Children with IBS have a greater percentage of class gammaproteobacteria. Furthermore, immune activation may play an important role in patients with IBS. As some of the effects of the microbiota on visceral pain responses are mediated viamicrobiota-neuroimmune interactions, changes of gastrointestinal flora could be a viable therapeutic option in FAP disorders. Beneficial effects of probiotics in IBS could be explained by reversing the imbalance between the pro and anti-inflammatory cytokines, enhancement of the intestinal mucosal barrier, and modulation of motility and visceral sensitivity. Administration of probiotic bacteria also has an impact on neuronal excitability and motility of gastrointestinal system(Lactobacillus reuteri).