Developments in analytical technology now allow the identification of some contaminants in milk that were not previously considered. It is critically important that mechanisms are devised to eliminate or reduce these contaminants below the maximum limit allowed by food safety regulations. Thus, the development, metabolization, measurement and reduction process of contaminants in milk must be understood and addressed. These processes are examined in this chapter through three case studies involving dietary iodine, veterinary medicines (specifically flukicides) and cleaning and disinfection agents containing chlorine as the active ingredient.