In the present study, we investigated nutritional status and health-related factors in a multistage cluster sample of 3119 Thai urban and rural children aged 0·5–12·9 years. In a subsample, blood samples were collected for the measurement of Hb, transferrin receptor, vitamin A and vitamin D concentrations. The prevalence of stunting and underweight was higher in rural children than in urban children, whereas the wasting rate was similar in both rural and urban areas. Among children aged 3·0–5·9 years, the prevalence of overweight was significantly higher in urban areas than in rural areas and so was the obesity rate in children aged 6·0–12·9 years. Protein intakes of all age groups were relatively high in both the areas. Intakes of Ca, Fe, Zn and vitamin C were significantly higher in urban areas than in rural areas. The prevalence of anaemia in rural areas was twice as high as that in urban areas, particularly in infants and young children. However, the prevalence of Fe-deficiency anaemia was similar in both urban and rural areas. While the prevalence of vitamin A deficiency (by serum retinol cut-off < 0·7 μmol/l) seemed to be very low, vitamin A insufficiency (by serum retinol cut-off < 1·05 μmol/l) was more prevalent (29·4–31·7 %) in both the areas. The prevalence of vitamin D insufficiency ranged between 27·7 and 45·6 % among the children. The present study indicates that the double burden of malnutrition is still a major public health problem in Thailand. Further studies need to explore the associated risk factors for these nutrient deficiencies. Effective strategies and actions are needed to tackle the nutritional problems in Thai children.