To empower local authorities to plan and evaluate adequate interventions, appropriate iodine deficiency disorders (IDD) indicators need to be identified. The aim of this study was to describe the magnitude and severity of IDD with different outcome indicators and associate them with functional indicators. Schoolchildren (n = 544) aged 8-10 y were assessed in 11 villages within five subdistricts of Malang District, East Java, Indonesia. Outcome indicators of IDD were goiter size as measured by palpation and ultrasonography (USG), urinary iodine excretion (UIE) and serum thyroid stimulating hormone (TSH) concentration in blood as well as functional indicators such as intellectual performance (IQ: Catell's Culture Fair Intelligence Test) and anthropometric indices. The total goiter rate (TGR) measured by palpation and USG were 35.7 and 54.4%, respectively. Based on UIE and TSH, the prevalence of iodine deficiency was 63.7 and 3.4%, respectively. In individuals, goiter, thyroid volume and UIE were associated significantly (r = -0.35; P < 0.001 and r = -0.30; P = 0.02 respectively). Among villages, TGR measured by palpation was significantly correlated with thyroid volume (r = 0.61; P = 0.045) and UIE (r = 0.68; P = 0.021), whereas TSH was not significantly associated with any of the observed indicators in individuals or groups. Multiple regression analysis showed that USG (beta = -0.67; P < 0.001) and UIE (beta = 4.39; P = 0.008) related significantly with cognitive performance (IQ). The associations between IDD indicators and cognitive performance and height-for-age Z scores suggest that socioeconomically advantaged children had better iodine status. We suggest that UIE is the best indicator for local authorities to assess iodine deficiency.