The aim of this study was to determine whether Saccharomyces boulardii prevents and treats diarrhoea and antibiotic-associated diarrhoea (AAD) in children. A total of 333 hospitalised children with acute lower respiratory tract infection were enrolled in a 2-phase open randomised controlled trial. During the 1st phase, all children received intravenous antibiotics (AB). They were randomly allocated to group A (S. boulardii 500 mg/day + AB, n=167) or group B (AB alone, n=166) and followed for 2 weeks. Diarrhoea was defined as ≥3 loose/watery stools/day during at least 2 days, occurring during treatment and/or up to 2 weeks after AB therapy had stopped. AAD was considered when diarrhoea was caused by Clostridium difficile or when stool cultures remained negative. In the 2nd phase of the study, group B patients who developed diarrhoea were randomly allocated to two sub-groups: group B1 (S. boulardii + oral rehydration solution (ORS)) and group B2 (ORS alone). Data from 283 patients were available for analysis. Diarrhoea prevalence was lower in group A than in group B (11/139 (7.9%) vs. 42/144 (29.2%); relative risk (RR): 0.27, 95% confidence interval (CI): 0.1-0.5). S. boulardii reduced the risk of AAD (6/139 (4.3%) vs. 28/144 (19.4%); RR: 0.22; 95% CI: 0.1-0.5). When group B patients developed diarrhoea (n=42), S. boulardii treatment during 5 days (group B1) resulted in lower stool frequency (P<0.05) and higher recovery rate (91.3% in group B1 vs. 21.1% in B2; P<0.001). The mean duration of diarrhoea in group B1 was shorter (2.31±0.95 vs. 8.97±1.07 days; P<0.001). No adverse effects related to S. boulardii were observed. S. boulardii appeared to be effective in the prevention and treatment of diarrhoea and AAD in children treated with intravenous antibiotics.