BACKGROUND The aim of this study was to investigate whether it is possible to modulate gut microflora and preserve intestinal barrier function during elective colorectal surgery by using combinations of oral antibiotics, synbiotics and mechanical bowel preparation (MBP). METHODS Ninety-two patients were randomly assigned to one of four groups. Group 1 had MBP only, group 2 had neomycin + MBP, group 3 had synbiotics + neomycin + MBP, and group 4 had synbiotics + neomycin but no MBP. Changes in gut microflora were assessed by culturing nasogastric aspirates and polymerase chain reaction-denaturing gradient gel electrophoresis of faecal samples. Intestinal barrier function was determined by microbiological confirmation of bacterial translocation and measurement of intestinal permeability. The inflammatory response was monitored by measurement of serum C-reactive protein and interleukin 6, and septic morbidity was recorded prospectively. RESULTS Four patients were excluded owing to protocol violation, leaving 24 patients in group 1, 22 in group 2, 20 in group 3 and 22 in group 4 for analysis. There was a significant decrease in Enterobacteriaceae in group 3 compared with the other groups. Group 3 had a significantly lower incidence of translocation after bowel mobilization (P < 0.001). There was no significant difference between the groups in intestinal permeability, inflammatory response or septic morbidity. CONCLUSIONS The combination of MBP, neomycin and synbiotics reduces the prevalence of faecal Enterobacteriaceae and bacterial translocation; however, this was not associated with a reduction in inflammatory response or septic morbidity in this study. Larger trials are needed before a change in practice can be recommended.