Stunting in school-age years may result in a decrease in adult size, and thus reduced work capacity and adverse reproductive outcomes. We have compared the mean intakes of energy, protein and selected growth-limiting nutrients in fifty-eight stunted children and 172 non-stunted controls drawn from 567 children aged 6–13 years attending ten rural schools in NE Thailand. Control children were selected randomly after stratifying children by age in each school. Dietary data were calculated from 24-h recalls using nutrient values from Thai food composition data and chemical analysis. Inter-relationships between stunting and sociodemographic, anthropometric and biochemical variables were also examined. Biochemical variables investigated were serum albumin, zinc, ferritin, transferrin receptor and retinol, and iodine in casual urine samples. Significantly more males than females were stunted (males, n 38, 65·5 % v. females, n 20, 34·5 %; P = 0·025). Stunted males had lower mean intakes of energy, protein, calcium, phosphorus and zinc, and a lower mean (95 % CI) serum zinc (9·19 (8·53, 9·84) v. 9·70 (8·53, 9·29) μmol/l) than non-stunted males; no other biochemical differences were noted. Stunted males also had a lower mean arm muscle area (P = 0·015), after adjusting for age, than non-stunted males. In conclusion, the lower dietary intakes of the stunted males compared to their non-stunted counterparts may be associated with anorexia and hypogeusia induced by zinc deficiency. Hence, zinc deficiency may be a factor limiting linear growth, especially among boys in NE Thailand, but more research is needed to establish whether other factors also play a role.