The current study added complete idea about different reasons related to increasing the disinfection by-products (DBPs). It also evaluated ratio of the individual by-products to the total organic halogen. The study suggested new methods to minimize some of these by-products. It also added new idea about effect of the different chlorine doses on the electrophoretic protein pattern. The most important goal of the study is suggestion of new disinfecting agent without DBPs to replace chlorine in the difficult conditions. The study covered effect of the new disinfecting agent on the electrophoretic DNA pattern and the different body functions at level of the experimental animals and compared it with effect of chlorine. Finally, the authors’ group added new experimental idea to change the traditional concepts of water treatment and water analysis to be applicable in all water treatment plants.