Probiotics, beneficial living microorganisms, have been proven to be effective in preventing gastrointestinal infections, but their effect in preventing urinary tract infection (UTI) is inconclusive. A prospective randomized controlled study was done to compare the preventive effect of probiotics with conventional antibiotics in children with persistent primary vesicoureteral reflux (VUR). One hundred twenty children who had had persistent primary VUR after antibiotic prophylaxis for 1 year were randomly allocated into a probiotics (Lactobacillus acidophilus 10(8) CFU/g 1 g b.i.d., n = 60) or an antibiotics (trimethoprim/sulfamethoxazole 2/10 mg/kg h.s., n = 60) prophylaxis group during the second year of follow-up. The incidence of recurrent UTI was 18.3% (11/60) in the probiotics group, which was not different from 21.6%(13/60) in the antibiotic group (P = 0.926). The causative organisms of recurrent UTI were not significantly different between the two groups (P = 0.938). Even after stratification by VUR grade, age, gender, phimosis, voiding dysfunction and renal scar, the incidence of recurrent UTI did not differ significantly between the two groups (P > 0.05). The development of new renal scar was not significantly different between the two groups (P > 0.05). In conclusion, probiotics prophylaxis was as effective as antibiotic prophylaxis in children with persistent primary VUR.