Aim: The aim of this study was to evaluate and compare the efficacy of 0.2% aqueous chlorhexidine gluconate (CHG) and 1% aqueous stabilized chlorine dioxide (ClO₂) mouthrinse as pre-procedural mouthrinses on colony forming unit (CFU) count from aerosols generated during ultrasonic scaling. Materials and methods: This prospective controlled parallel arm clinical and microbiological study done over a period of 2 months included 60 systemically healthy participants with no signs of gingivitis or periodontitis divided into 3 groups (1 to 3) with 20 participants each receiving CHX, ClO2 and normal saline as control respectively as pre-procedural rinses followed by collection of aerosols generated during ultrasonic scaling on agar plates kept at three positions namely patient (P), operator (O) and assistant (A) and incubated for 24 hours at 37^oC. The CFUs were then counted and statistically analyzed. Results: Data for the inclusion criteria of plaque index (PI) for all 60 subjects (mean 0.5088 ± 09001) presented normal distribution (p = 0.200). The mean and standard deviation values of retrievable CFUs for all three treatment groups 1 to 3 at three positions of P, A and O were performed using one way ANOVA test with intergroup comparison between by Tukey HSD test. Highest reduction in CFUs was seen in CHX group followed by ClO₂ followed by normal saline which showed least reduction in CFU counts. Conclusion: It was concluded that aqueous 0.2% CHX was more efficacious in reducing retrievable CFU counts when compared to aqueous 1% stabilized chlorine dioxide mouthrinse and normal saline when used as pre-procedural mouthrinses. Limitations: As only aerobic culture was done to assess the CFU counts, anaerobic culture would have added more value to the study as it can influence the retrievable CFU counts. Also, despite of best efforts to standardize the settings in dental operatory, there could be some degree of variability.