Disinfection for drinking water reduces the risk of pathogenic infection but may pose chemical threat to human health due to disinfection residues and their by-products when the organic and inorganic precursors are present in water. Administration of huwa-san through drinking water or by oral injection caused alterations in the biochemical functions of the liver and kidney more than chlorine. The lipid profile showed that both of chlorine and huwa-san caused disturbances in the lipids. This was represented by elevation in the triglycerides. So, the lipid became more susceptible to be oxidized by the free radicals generated by chlorine and huwa-san. The ultrastructure showed that administration of chlorine and huwa-san caused structural abnormalities in the liver and kidney surfaces. The chlorine administration caused more severe damages in the liver and kidney than huwa-san at the same dose and by the same administration way. The administration of huwa-san caused more alterations in the biochemical liver and kidney functions than chlorine. The chlorine caused changes in the liver and kidney ulrastructure than huwa-san.