The underlying genetic components contributing to individual variability in functions of the stress responsive hypothalamic-pituitary-adrenal (HPA) axis are poorly understood. To determine genetic loci mediating three aspects of the adrenocortical function, we conducted a quantitative trait loci (QTL) analysis in the segregating F2 generation of a Wistar Kyoto (WKY) x Fisher 344 (F344) cross, two inbred rat strains that differ in several HPA axis measures. The following three components of adrenocortical function are known to be regulated by different mechanisms which are mediated via suprahypothalamic, hypothalamic, pituitary and intraadrenal influences: basal plasma corticosterone (CORT) levels, plasma CORT response to a 10 minute restraint stress and adrenal weight. Genome scans identified a complex genetic architecture for the basal CORT phenotype including sex and maternal lineage effects. Pairwise interactions were also identified for this trait. We identified three significant and two suggestive QTL for stress CORT, along with two pairs of interacting loci for this trait. Four highly significant and two suggestive loci were identified for adrenal weight, with no interacting loci. In contrast to basal CORT, no sex- or lineage dependent QTL were identified for stress CORT or adrenal weight, despite the large sex differences in these phenotypes. We identified three nucleotide alterations in an obvious candidate gene mapped to the most significant QTL for stress CORT, corticosterone binding globulin (CBG), one of which is known to alter CBG binding. This analysis confirms that three separate traits regulated by the HPA axis are controlled by multiple, but mainly non-overlapping QTL.