Chlorhexidine oral rinse treats bacterial gum disease (gingivitis) by killing or preventing the growth of bacteria, which helps to reduce inflammation and reduce bleeding of your gums. The medication is used along with regular tooth brushing and flossing to treat gingivitis. This medication has been used to prevent tooth decay in those who are unable to brush their teeth and is used in those with weakened immune systems to decrease the formulation of mouth sores (mucositis).