OBJECTIVE To evaluate the incidence of small bowel bacterial overgrowth (SBBO) in children treated with omeprazole, and to test whether probiotics influence the incidence. METHODS A double-blinded, placebo-controlled trial was performed in 70 children treated orally during four weeks with 20mg omeprazole per day. Lactobacillus rhamnosus R0011 (1.9×10(9) cfu) and Lactobacillus acidophilus R0052 (0.1×10(9) cfu) were simultaneously given daily to 36 subjects (probiotic group), while 34 subjects received placebo (placebo group). The diagnosis of SBBO was based on the development of suggestive symptoms, in combination with a positive glucose breath test. RESULTS After one month of proton pump inhibitor (PPI) treatment, 30% (21/70) had a positive breath test suggesting SBBO; of these 62% were symptomatic. Five children developed SBBO-like symptoms, but had a negative breath test; and 44 (63%) were symptom free and had a negative breath test. There was no difference in the incidence of positive breath tests in the probiotic versus the placebo group (33% vs 26.5%; p=0.13). CONCLUSIONS Since symptoms suggesting SBBO developed in 26% of PPI-treated children, and since the glucose breath test was abnormal in 72% of these, this side-effect should be more frequently considered. The probiotic tested did not decrease the risk to develop SBBO.