AbstractUndernutrition is a stressor with long-term consequences, and the effect of nutritional recovery on cortisol and thyroid hormone status is unknown. To investigate basal thyroid hormones and the cortisol response to a cold pressor test in children recovered from undernutrition, a cross-sectional study was undertaken on children (6–16 years) separated into four groups: control (n 41), stunted (n 31), underweight (n 27) and recovered (n 31). Salivary cortisol was collected over the course of 10 h: upon awakening, before and after an unpleasant and a pleasant stimulus. Cortisol upon awakening was highest in the stunted and lowest in the underweight groups: control=5·05 (95 % CI 3·71, 6·89) nmol/l, stunted=6·62 (95 % CI 3·97, 11·02) nmol/l, underweight=2·51 (95 % CI 1·75, 3·63) nmol/l and recovered=3·46 (95 % CI 2·46, 4·90) nmol/l (P=0·005). Girls had higher cortisol concentrations upon awakening compared with boys (P=0·021). The undernourished groups showed an elevated cortisol response both to the unpleasant stimulus and at the last measurement (16.00 hours) compared with that of the recovered group: AUC, control=2·07 (95 % CI 1·69, 2·45) nmol/l×30 min, stunted=2·48 (95 % CI 1·91, 3·06) nmol/l×30 min, underweight=2·52 (95 % CI 2·07, 2·97) nmol/l×30 min, recovered=1·68 (95 % CI 1·26, 2·11) nmol/l×30 min (P=0·042); and control=2·03 (95 % CI 1·75, 2·39) nmol/l×30 min, stunted=2·51 (95 % CI 1·97, 3·19) nmol/l×30 min, underweight=2·61 (95 % CI 2·16, 3·16) nmol/l×30 min, recovered=1·70 (95 % CI 1·42, 2·03) nmol/l×30 min (P=0·009). Lower free thyroxine (T4) was found in the recovered and stunted groups: control=1·28 (95 % CI 1·18, 1·39) pmol/l, stunted=0·98 (95 % CI 0·87, 1·10) pmol/l, underweight=1·10 (95 % CI 1·01, 1·21) pmol/l and recovered=0·90 (95 % CI 0·83, 0·99) pmol/l (P<0·001). Multivariate analysis showed a lower cortisol concentration along 10 h (06.00–16.00 hours) in the recovered compared with the other groups (P=0·017), and similar concentrations between the recovered and control group. In conclusion, the children with recovery in weight and height had a cortisol stress response similar to control but a lower basal free T4. Longitudinal studies are warranted to determine the extent of these endocrine changes after recovery of undernutrition and in adulthood.