The goal of this study was to use BxD recombinant inbred mice to search for genes that control the hypothalamic corticotrophin releasing factor (CRF) system. The specific phenotype that was measured was abundance of transcripts that encode CRF, CRF receptor (Crf-R1), CRF binding protein (Crf-BP) and argenine vasopressin (AVP) in total hypothalamic RNA. The strain distribution patterns (SDP) for the transcript abundances for each target were continuously distributed, consistent with these being quantitative traits. Marker regression and interval mapping revealed associations with quantitative trait loci (QTL) for CRF transcript abundance (CRFta) on chromosome 1 (at 89.2 centiMorgan (cM)), chromosome 12 (between 54 and 58cM) and chromosome 13 (between 26 and 30 cM); for Crf-R1ta on chromosome 7 (at 1.5 cM), chromosome 12 (at 37 cM) and chromosome X (at 30 cM); for Crf-BPta on chromosome 7 (at 48.5 cM), chromosome 8 (at 65 cM), and chromosome 12 (at 19 cM); and for AVPta on chromosome 7 (at 1cM), chromosome 12 (at 13 cM) and chromosome 13 (at 45cM). The transcript abundance QTL were not linked to their respective structural genes. Interval mapping on chromosome 7 reveals substantial overlap between QTL that control AVP and Crf-R1 transcript abundance and on chromosome 12 for QTL that control CRF and Crf-R1, which may indicate loci that coordinate regulation of the CRF system. There are QTL for all four targets on chromosome 12. There are a number of neurodevelopmental genes in very close proximity to the transcript abundance QTL that are potential candidate genes.