Chlorhexidine (0.2%) is a ‘Gold Standard’ which is commercially available and effective mouth rinse which inhibits supragingival plaque formation and also reduction in the population of S. mutans after rinsing daily. Lately, it has been proved that the force of magnetism has a great influence on the living organism. Magnetized water has its effect on human body when taken regularly for a considerable period but its use in dentistry is still lacking. Aim: This study was done to evaluate antibacterial efficacy and effect of dosage, frequency and duration of commercially available 0.2% chlorhexidine mouth rinse and conventionally prepared magnetized water on colony count of S. mutans. Materials and methods: A total of 50 subjects were selected between the age group of 5 to 12 years. A baseline sample was collected before starting with rinses. Then the subjects were divided in four major groups. Group I was chlorhexidine, group II was subdivided into group IIA and group IIB which were magnetized water groups (24 hours of magnetization) rinsing for 1 minute and 3 minutes respectively and group III was magnetized water (72 hours of magnetization) group rinsing for 3 minutes. The samples were collected and sent to microbiological laboratory for S. mutans count. Results: The obtained values of all the groups were subjected to statistical analysis. Conclusion: The reduction of S. mutans count of group III was almost in par with group I.