Variations in the expression levels of bone marker genes among the inbred strains of mice in response to mechanical loading (ML) are largely determined by genetic factors. To explore this, we performed four-point bending on tibiae of 10-week female F2 mice of B6XC3H cross using 9N at 2 Hz, 36 cycles, once per day for 12 days. We collected tibiae from these mice for RNA extraction. We then measured the expression changes of bone marker genes, bone sialoprotein (BSP), alkaline phosphatase (ALP) and housekeeping genes, beta-actin and peptidylprolyl isomerase A (PPIA), by using real-time PCR in both the loaded and the non-loaded tibiae of F2 mice (n=241). A genome-wide scan was performed using 111 micro satellite markers in DNA sample collected from these mice. Mean increase in gene expression, expressed as fold change, ranges from 2.8 to 3.0 for BSP and 2.7 to 2.8 for ALP. Both showed a skewed distribution with a heritability response of 87 to 91%. Absence of significant correlation between the increased gene expression vs. body weight (BW) and bone size (BS) suggests that bone response to loading is independent of BS or BW. Non-parametric mapping (MapQTL program 5) revealed that BSP and ALP expression in response to bending was regulated by several significant and suggestive QTL: Loci regulating both BSP and ALP were located on Chr 8 (60.1 cM), 16 (45.9 cM), 17 (14.2 cM), 18 (38.0 cM) and Chr 19 (3.3 cM); Loci specific to BSP were found on Chrs 1 (LOD score 10.4 at 91.8 cM), 5 (5.2 at 73.2 cM) and 9 (7.0 at 13.1 cM); Loci regulating only ALP were found on Chrs 1 (7.6 at 46 and 75.4 cM), 3 (8.3 at 47 cM) and 4 (5.6 at 54.6 cM). QTLs on Chrs 1, 3, 8, 9, 17 and 18 correspond to QTLs we previously reported by pQCT measurements, thus validating these findings. In addition, we found that the QTL associated with non-loaded tibiae for BSP and ALP on Chrs 4, 16 and 18 was identical to the QTLs associated with ML. This finding suggests that regions on these chromosomes are responsible for natural variation in expression of BSP and ALP as well as for ML. This is the first expression study to provide evidence for the presence of multiple genetic loci regulating bone anabolic response to loading in the B6XC3H intercross and will lead to a better understanding of how exercise improves the skeletal mass.