Iodine deficiency can cause goitre, cretinism, decrease of intellegence, mental retardation, brain damage, deaf-mutism, and cause miscarriage in pregnant women and stillbirth as well. The method of high performance liquid chromatography (HPLC) ion pair was used in this research can separate and determine iodine species i.e. iodide and iodate specificaly, accurately and precisely. The Results were showed the development of reliable analytical method by ion pair high performance liquid chromatography for the determination of iodine species content in iodized salt during storage. Another new insight was concerning some factors that influenced the decomposition of iodate into other iodine species and the stability of iodate in iodized salt and food.