Abstract: Objective To explore the changes of intestinal microbiota in children with benign infantile convulsions associated with mild gastroenteritis (BICE). Methods Forty-five cases of BICE diagnosed in our hospital between January, 2013 and December, 2016 were the study group. Forty-five cases of acute gastroenteritis diagnosed in our hospital between January, 2013 and December, 2016 were the control group. Fecal rotavirus was detected and Escherichia coli, Enterococcus, Lactobacillus and Bifidobacterium were cultured in the two groups. Fasting venous blood was phlebotomized and intestinal mucosal barrier indexes including diamine oxidase (DAO), nitric oxide (NO) and D-lactic acid were measured. Results The positive rate of fecal rotavirus in the study group (48.9%) was significantly higher than that in the control group(26.7%), P<0.05. The amounts of Escherichia coli[(7.8±2.3) CFU/g], Enterococcus[(6.0±2.3) CFU/g], Lactobacillus[(4.9±1.7) CFU/g] and Bifidobacteria[(5.1±1.5) CFU/g] in the study group were lower than the amounts of Escherichia coli[(8.8±2.2) CFU/g], Enterococcus[(7.3±2.8)]CFU/g, Lactobacillus[(6.0±2.5) CFU/g] and Bifidobacteria[(5.9±1.9) CFU/g]in the control group (P<0.05). The serum level of DAO[(9.84±4.17) U/L], D-lactic acid[(0.92±0.39) mmol/L] and NO[(126.8±48.1) μmol/L] in the study group were significantly higher than the serum level of DAO[(7.49±2.73) U/L], D-lactic acid[(0.73±0.25) mmol/L] and NO[(0.73±0.25) μmol/L] in the control group. Conclusion Rotavirus is closely associated with the pathogenesis of BICE. Probiotics in intestinal tract of BICE children reduce and intestinal mucosal barrier function decrease, which means supplement of probiotics may help to prevent and treat BICE.