Individual differences in the level of the stress hormone cortisol play a prominent role as an explanatory variable in studies on psychopathology. Relatively few studies have paid attention to individual differences in cortisol levels and the etiology of these differences, in particular their possible genetic basis. All these studies have been in adults. The aim of this study was to estimate genetic and environmental influences on basal cortisol levels in 12-year-old children. To this end, four samples of salivary cortisol were collected on two consecutive days in a sample of 180 twin pairs. Low correlations were found between cortisol levels at different points in time during the day. A significant genetic contribution was found to the variation of basal cortisol levels in the morning and afternoon samples, but not in the evening sample. Heritability did not differ for boys and girls and was highest (60%) for cortisol levels during the sample taken about 45 minutes after awakening. This cortisol awakening response provides a useful endophenotype in the search for genes that may affect hypothalamic-pituitary adrenocortical functioning in children.