Recurrent urinary tract infection (UTI) in children is a well-known risk factor of chronic kidney disease. Periurethral area is normally inhabited by non-pathogenic flora, such as Bifidobacterium sp., and pathogenic flora from gastrointestinal tract, such as Escherichia coli (E. coli), which can cause UTI. Dysbiosis between pathogenic and non-pathogenic bacteria leads to infections, but studies regarding dysbiosis and recurrent UTI have not yet been documented. To estimate the proportional differences between gastrointestinal E. coli and Bifidobacterium sp. in children with recurrent UTI, a cross-sectional study was conducted in children from age six months to <18 years old diagnosed with recurrent UTI in Dr. Cipto Mangunkusumo Hospital. Healthy children matched in gender and age were recruited as control group. Stool samples were obtained from all the children in the two groups. Stool DNA was extracted using real-time polymerized chain reaction method to count E. coli and Bifidobacterium sp. proportion. Children with recurrent UTI had significantly higher proportion of E. coli compared to control group (10.97 vs. 4.74; P = 0.014) and lower proportion of Bifidobacterium sp. (6.54 vs. 9.33; P = 0.594). In children with recurrent UTI group, E. coli proportion was found higher than Bifidobacterium sp. although not statistically significant (10.97 vs. 6.54; P = 0.819). In healthy controls, Bifidobacterium sp. proportion was significantly higher than E. coli (4.74 vs. 9.33; P = 0.021). The total amount of E. coli (996,004 vs. 1,099,271; P = 0.798) and Bifidobacterium sp. (835,921 vs. 1,196,991; P = 0.711) were higher in secondary UTI compared to the simple UTI. Proportion of E. coli is higher in children with recurrent UTI than in healthy children. The proportion of E. coli is higher than Bifidobacterium sp in the colon of children with recurrent UTI.