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Background: Chlorhexidine mouth rinse, a 'Gold Standard'effective in reducing plaque and gingivitis, has some drawbacks like bitter taste, light brown staining of teeth etc. limiting its long-term use. Magnetized water is alkaline and inhibits the bonding process between plaque and teeth by “magnetohydrodynamic”. Aim: To compare and evaluate effectiveness of magnetized water and 0.2% chlorhexidine as a mouth rinse in children aged 12-15 years for plaque and gingivitis inhibition during 3 weeks of supervised use. Settings and Design: This was a double blinded randomized control clinical study, carried out at a non-government high school. Methods:A total of 20 children aged 12-15 years were randomized into two groups, magnetized water and 0.2% chlorhexidine, each comprising of 10 children who were asked to rinse with the respective mouthwash. Plaque index (PI) scoresand gingival (GI) scoreswere evaluated at baseline, 2 weeks and at 3 weeksfor each child. Statistical analysis: Independent sample t test and paired sample t test were used to check the mean differences. Result: A statistically significant difference was found in reduction of mean PI and GI scores of magnetized water (p=0.0001) and Chlorhexidine groups(p=0.0001) both at 14 days (2 weeks) and at 21 days (3 weeks) with no adverse effects. Conclusion: Daily use of magnetized water as a mouth rinse was safe andeffective alternative to chlorhexidinein plaque and gingivitis reduction, which supplemented the benefits of daily toothbrushing in children.