Background: Goiter is thyroid enlargement, which is the most common visible symptom of iodine deficiency. Some studies have shown iodine deficiency in water, soil, and food in many places worldwide.We aimed to determine the prevalence of goiter and the association between urine iodine levels in children with severity and prevalence of goiter in mountainous villages of Kashan city (center of Iran). Methods: This descriptive-analytical study was performed on 263 children aged 6-12 years in villages of Kashan. In the present study, goiter and its grading was determined by WHO standard method. The patients’ urine iodine levels were measured by Pino method (ammonium oxidation) and compared with standard scales. Results: Of the children, 39.5% had goiter and the prevalence in girls was higher than boys (45.8% v 33.3%; P<0.03). All the patients with urine iodine level less than 25 µg/grcr (gram creatinine), 87.5% of patients with urine iodine level less than 100 µg/grcr and 24% of patients with urine iodine level more than 100 μg/grcr had goiter. Conclusion: The prevalence of goiter in mountainous places of Kashan is 39.5%. Although the people of these villages used iodized salt for years, these regions remain endemic parts of iodine deficiency. There was a significant association between urine iodine levels and the severity and prevalence of goiter (P< 0.001).