Background: The standard practice in many institutions incorporates nasopharyngeal probes for temperature monitoring in patients undergoing general anaesthesia. Current disinfection guidelines for these devices are not clear and they are poorly adhered to. In South Africa, these temperature probes are reused and subjected to unstandardized decontamination processes. This study sought to investigate nasopharyngeal temperature probes as possible source for cross-contamination, and assess the efficacy of current disinfection practices for these probes. Methodology: This was an analytical double-blind randomized study of 4 different disinfection protocols for 48 nasopharyngeal temperature probes. The probes were randomized to disinfection protocols that included water wash, dry wipe, hibitane® and cidex® wash. After decontamination by the respective protocol, the probes were aseptically placed in nutrient broths, manually agitated and removed, and the broths were then inoculated onto blood agar plates. After 48 hours of aerobic culture incubation at 37oC, plates were examined for growth and bacteria identified using automated bioMérieux Vitek-2 microbial identification system. Chi square and logistic regression analyses were used to assess bacterial contamination rates of the disinfected probes, in order to infer the efficacy of the decontamination processes. Results: Of the 48 nasopharyngeal temperature probes disinfected by the different protocols, 22 (45.8%) had bacterial contamination, with frequency of isolation for coagulase negative staphylococci (44%), Bacillus cereus (20%), Staphylococcus aureus (10%), Enterobacter cloaca (7%), Pseudomonas aeruginosa (4%), Pseudomonas fluorescens (3%), Acinetobacter baumannii (3%), amongst other bacterial species. Dry wipe, and water and soap methods, had statistically significant higher contamination rates of 83.3% and 66.7% than hibitane® and cidex®, with 25.0% and 8.3% respectively (X2=17.69, p<0.0001). The odds of contamination when water-wipe was used as a cleaning method was 6 times (OR=6.000; 95% CI=1.018-35.374, p=0.048) that of hibitane® method while the odds for dry-wipe was 15 times (OR=15.000, 95% CI=2.024-111.174, p=0.008). No statistically significant difference was observed in the contamination rates between cidex® and hibitane® disinfection methods(OR=0.273, 95% CI=0.024-3.093, p=0.294). Conclusion: These data shows that nasopharyngeal temperature probes are possible source of cross-contamination and pathogen transmission due to inadequacy of the decontamination processes for these temperature probes.