Bone formation and growth are controlled by genetic, hormonal and biomechanical factors. In this study, an established rat disuse osteoporosis model, hindlimb-suspension (HLS), was used to relate morphological change and gene expression to altered mechanical load in the underloaded femora and the ostensibly normally loaded humeri of the suspended rats (39 days old at onset; 1, 3, 7 and 14 days suspension). Morphological change was measured by labelling new bone formation with fluorescent agents during the experimental period and subsequent histological analysis of bone sections post-sacrifice. Hindlimb suspension reduced both the total amount of bone present, assessed as cross-sectional area, and the bone formation rate at the mid-diaphysis of the unloaded femora while no significant effect was found in the loaded humeri. In addition, the femora of the suspended animals were found to have a markedly increased circularity as a result of unloading. A sensitive semi-quantitative method of gene expression analysis, involving the creation of SMART cDNA arrays, was successfully implemented. This technique amplified all populations of mRNA to levels where they could be assessed using standard molecular biology protocols. Gene expression patterns of two candidate genes, c-fos and osteocalcin were assessed in periosteal tissue. Altered gene expression patterns were identified and tracked over the suspension period. The altered levels of both candidate genes were found to be consistent with the changes observed in the histological analysis.