This randomised prospective study aimed at evaluating possible differences in the post-operative complication rate following lower wisdom tooth surgery performed with either sterile or clean surgical gloves. The microbiological profiles of the tooth sockets and glove surfaces were also evaluated and compared. A total of 275 ASA I, non-smoking and non-drinking patients consented to be randomly assigned into two groups for lower wisdom tooth surgery, performed by operators wearing either sterile or clean gloves. All the patients returned for a post-operative assessment visit one week later. An additional 40 patients were recruited and randomised into the sterile glove group (n = 20) or the clean glove group (n = 20) for the microbiology study. Specimens were taken from the glove surfaces and the post-operative socket wounds during wisdom tooth surgery. This clinical trial showed no significant difference between the sterile and clean glove groups in the incidence of acute inflammation, acute infection and dry sockets in the wounds. No single peri-operative factor had a statistically significant effect on post-operative pain intensity. Most of the bacterial isolates from the clean gloves were Gram-positive cocci or spore-forming bacilli. The total number of colony forming units and the variety of bacterial isolates from the socket wounds in the sterile and clean glove groups were similar. The study concluded that there was no advantage in using sterile surgical gloves rather than clean gloves to minimize post-operative complications in wisdom tooth surgery. There was also no apparent relationship between the bacteria contaminating the clean glove surfaces and those isolated from the socket wounds.