Drinking water is the major natural source of iodine in many European countries. In the present study, we examined possible sites of iodine loss during the usual water purification process. Water samples from 6 sites during the technological process were taken and analyzed for iodine content. Under laboratory circumstances, prepared iodine in water solution has been used as a model to test the effect of the presence of chlorine. Samples from the purification sites revealed that in the presence of chlorine there is a progressive loss of iodine from the water. In the chlorine concentrations employed in the purification process, twenty four hour chlorine exposure eliminated more than 50% of iodine when the initial iodine concentration was 250 μg/L or less. Iodine was completely eliminated if the starting concentration was 16 μg/L. We conclude that chlorine used during water purification may be a major contributor to iodine deficiency in European communities.