The aim of this study was to investigate the degree of contamination of a surgeon's hand following use of chlorhexidine gluconate or alcohol gel as disinfectants. In this prospective, randomised trial, orthopaedic surgeons were allocated to one of two different hand-washing protocols using a randomisation table. The hand-washing protocol dictated that all surgeons should wash for 5 min with chlorhexidine for their first case. Thereafter, the surgeon was randomised to wash for 3 min with either alcohol gel or chlorhexidine. At the end of each procedure, the gloves of each surgeon were carefully removed and the fingertips from each hand were placed on an agar plate. The number of bacterial colonies present after 24 h and 48 h of incubation were recorded for each agar plate by a microbiologist blinded to the washing protocol used. Overall, 41 procedures and 82 episodes of hand washings were included in the study. Two episodes were discarded due to contamination at the time of glove removal. Four hands (8%) were contaminated in the chlorhexidine group compared to 19 (34%) in the alcohol group. Fisher's exact test confirmed a significantly higher risk of contamination using alcohol gel compared to chlorhexidine (P = 0.002). In addition, the average bacterial colony count was substantially higher in the alcohol group (20 colony forming units) compared to the chlorhexidine group (5 colony forming units). There was no relationship between the duration of surgery and the degree of contamination (P = 1.12). Alcohol gel disinfectant is not a suitable alternative to chlorhexidine when hand washing before surgery. This study has identified a higher risk of bacterial contamination of surgeons' hands washed with alcohol. This may lead to higher levels of postoperative infection in the event of glove perforation.