Background & objectives: The present investigation was undertaken to study the iodine nutritional status of school children of Imphal east district in Manipur where endemic goitre persists during post-salt iodization phase along with the investigation of the factors responsible for the occurrence of goitre endemicity. Methods: A total of 1,286 children (6-12 yr) were clinically examined for goitre from study areas of Imphal east district. A total of 160 urine samples were collected and analyzed to measure urinary iodine and thiocyanate levels. Iodine content was measured in 140 salt samples and 16 drinking water samples. Results: Overall goitre prevalence was about 30 per cent (grade 1-24.7%; grade 2-5.3%) and median urinary iodine level was 17.25 μg/dl. The mean urinary thiocyanate level was 1.073 ± 0.39 mg/dl. Iodine/ thiocyanate ratio (μg/mg) was in the ranges from 15.65 to 22.34. The mean iodine content in drinking water samples was 2.92 ± 1.75 μg/l and 97.8 per cent of edible salts had iodine level above 15 ppm at the consumption point. Interpretation & conclusion: Our findings showed that in spite of no biochemical iodine deficiency, iodine deficiency disorders (IDD) is a serious public health problem in Imphal east district of Manipur. The consumption pattern of certain plant foods containing thiocyanate (or its precursors) was relatively high that interfere with thyroid hormone synthesis resulting in the excretion of more iodine. Thus, the existing dietary supplies of thiocyanate in relation to iodine may be a possible aetiological factor for the persistence of endemic goitre in the study region during post salt iodization period.