Surgical site infection after heart surgery increases morbidity and mortality. The method of presurgical hand disinfection could influence the infection risk. From February to April 2003, we compared the microbiological efficacy of hand-rubbing (R) and hand-scrubbing (S) procedures. The surgical team alternately used hand-scrubbing or hand-rubbing techniques every two weeks. Fingertip impressions were taken before and immediately after hand disinfection, every 2h and at the end of the operation. Acceptability of hand rubbing was assessed by a questionnaire. Mean durations of surgical procedures were 259+/-68 and 244+/-69min for groups S and R respectively (P=0.43). Bacterial counts immediately after hand disinfection were comparable with the two techniques, but significantly lower in group R at the end of surgery. No differences were observed between the percentages of negative samples taken after 2h, 4h and at the end of surgery between the two groups. Bacterial skin flora reduction immediately after hand disinfection, after 2h and 4h of operating time and at the end of surgery was better in group R, but the difference was not statistically significant. Before surgery, the hand-rubbing method with alcohol solution preceded by hand washing with mild neutral soap is as effective as hand scrubbing to reduce bacterial counts on hands. It decreased the bacterial counts both immediately after hand disinfection and at the end of long cardiothoracic surgical procedures. The acceptability of hand rubbing was excellent and it can be considered to be a valid alternative to the conventional hand-scrubbing protocol.