I prophylaxis is the most effective strategy to eradicate I deficiency disorders, but it has been shown to affect the thyroid disease pattern. In this study, we assessed the frequency of thyroid disorders in an adult population living in two areas of southern Italy after implementing I prophylaxis. To this aim, a cross-sectional, population-based study including 489 subjects from an I-deficient rural and an I-sufficient urban area of southern Italy was conducted. Thyroid ultrasound was performed on all participants, and urine and blood samples were collected from each subject. The levels of thyroid-stimulating hormone (TSH), thyroglobulin (TgAb) and thyroperoxidase antibodies (TPOAb), urinary I excretion (UIE), and thyroid volume and echogenicity were evaluated. We found that the median UIE was higher in the urban than in the rural area (P= 0.004), whereas the prevalence of subjects affected by goitre was higher in the rural compared with the urban area (P= 0.003). Positive TgAb rather than TPOAb were more frequent in subjects from the urban area compared with the rural area (P = 0.009). The hypoechoic pattern at thyroid ultrasound (HT-US) was similar between the two areas, but TgAb were significantly higher (P= 0.01) in HT-US subjects from the urban area. The frequency of elevated TSH did not differ between the two screened populations, and no changes were found for TgAb positivity in subjects with high TSH in the urban compared with the rural area. Our findings support that the small risks of I supplementation are far outweighed by the substantial benefits of correcting I deficiency, although continued monitoring of populations is necessary.