Iodine deficiency is a major determinant of endemic goiter which affects bone growth. The purpose of this study was to clarify the relationship between iodine deficiency and oral health. A cross-sectional survey was carried out on 181 inhabitants aged 17 to 40 years in two villages in an iodine-deficient area in Bali, Indonesia. Thyroid swelling, serum level of thyroid-stimulating hormone, DMFT index, plaque index, gingival index, dietary habits and socioeconomic status were examined. Thirty two subjects (21%) had thyroid swelling considered to be endemic goiter, with the highest prevalence in females aged 21 to 30 years (40-41%). The DMFT, food habits, and socioeconomic status were different between both villages. Multiple regression analysis adjusted for age, sex, and location (village) did not detect any association between DMFT and serum thyroid-stimulating hormone level or thyroid swelling. Further studies will be required to confirm these findings.