Iodine deficiency disorders (IDD) have remained an unresolved public health problem in India. In this survey, we have estimated the prevalence of IDD among 6-12 years of school children in rural areas of north Karnataka, India and estimated the prevalence of low iodine content (<15 ppm) in salt at the household level and urine iodine excretion in this population. In this cross-sectional survey, we recruited 16,827 children between 6 and 12 years of age through multistage sampling from six districts. Goitre was examined clinically for all children. Household-level salt iodine estimation and urinary iodine estimation were carried out among a subset of the participants. Overall prevalence of goitre was 17.1% (95% CI: 16.5, 17.7). Out of this, 76.7% (n = 2116) had Grade-1 goitre, and 23.7% (n = 656) had Grade-2 goitre. The prevalence of goitre was higher among females (17.9%, vs. male 16.4%, P < 0.05). The prevalence of low iodine content (<15 ppm) in salt was 48.5% (95%CI: 46.7, 50.3). The overall median iodine excretion in urine was 85 μg/L (IQR: 60-150 μg/L). In total, 37.2% (n = 601) had mild iodine deficiency, 5.2% (n = 84) had moderate deficiency, and 10.1% (n = 163) had severe deficiency. All parameters showed high inter- and intradistrict variations. North Karnataka has a high goitre prevalence. Low use of iodized salt can be a major reason for the high prevalence of the condition. Ensuring the availability of iodized salt in this region and periodic surveillance to measure the impact of the programme should be the priority in this region.