BackgroundDeficiencies of iodine and iron may have adverse effect on thyroid function. This study was undertaken to investigate the association between iron status and thyroid function in Nepalese children living in hilly regions.MethodsA cross-sectional study was conducted among 227 school children aged 6–12 years living in hilly regions of eastern Nepal. Urine and blood samples were analyzed for urinary iodine concentration, free thyroxine, free triiodothyronine, thyroid stimulating hormone, hemoglobin, serum iron and total iron binding capacity, and percentage transferrin saturation was calculated.ResultsThe cohort comprised euthyroid (80.6 %, n = 183), overt hypothyroid (1.3 %, n = 3), subclinical hypothyroid (16.3 %, n = 37) and subclinical hyperthyroid (1.8 %, n = 4) children respectively. About 35.2 % (n = 80) children were anemic, 43.6 % (n = 99) were iron deficient and 19.8 % (n = 45) had urinary iodine excretion < 100 μg/L. Hypothyroidism (overt and subclinical) was common in anemic and iron deficient children. The relative risk of having hypothyroidism (overt and subclinical) in anemic and iron deficient children was 5.513 (95 % CI: 2.844−10.685, p < 0.001) and 1.939 (95 % CI: 1.091-3.449, p = 0.023) respectively as compared to non-anemic and iron sufficient children. Thyroid stimulating hormone had significant negative correlation with hemoglobin (r = −0.337, p < 0.001) and transferrin saturation (r = −0.204, p = 0.002).ConclusionsThyroid dysfunction, iron deficiency and anemia are common among Nepalese children. In this cohort, anemic and iron deficient children had poor thyroid function.