Paediatric primary musculoskeletal (MS) cancers such as Ewing’s sarcoma and osteosarcoma account for 5% of childhood malignancies in the UK. Despite advances in surgical intervention and chemotherapy, the survival of patients with these malignancies has not improved substantially over the last 20 years. Current knowledge of the genetic drivers controlling the progression of MS cancers is very limited. Osteosarcoma also affects dogs and the pathology and pathogenesis of the canine disease bares remarkable similarity to the human variant. In dogs and humans, lung metastasis is the main cause of morbidity and mortality, and over 80% of cases have clinically undetectable microscopic metastasis at diagnosis. In addition, the progression to metastatic disease limits the 5-year survival rates to only 60-75%. Murine models are invaluable tools to study and improve the understanding of disease progression and pathogenesis. Several MS cancer cell lines have been characterised in vitro and in vivo, but a clinically relevant mouse model of musculoskeletal tumors model with spontaneous metastasis has not been validated. The aim of this thesis research was to develop a robust experimental pipeline to study the molecular drivers of metastasis, applicable across multiple musculoskeletal tumors. Here, the experimental model has been applied to the molecular mechanics of Ewing’s sarcoma as well as human and canine osteosarcoma. An established murine orthotopic model was utilised to demonstrate significant differences in gene expression in the pulmonary (secondary) lesion compared the primary tumour growing in the tibia in the same animal and shed light on mechanisms driving metastasis. Using fluorescent activated cell sorting (FACS), it was possible to isolate viable tumor cells from 100% of the tissues identified as being positive by in-vivo bioluminescent imaging. The FACS-based method allows for selective isolation of tumor cells from primary and secondary sites as well as from circulating tumor cells in the blood and enables high-throughput downstream genomic analysis. Using RNA-sequencing it was possible to identify over 1000 genetic targets involved in metastasis in canine osteosarcoma. In further work we went on to use CRISPR-Cas9 to selectively disrupt target expression and assess the resulting phenotype in vitro and in vivo. By applying the experimental pipeline to Ewing’s sarcoma, we identified 124 novel gene to be involved in the metastatic cascade. In addition, we have consolidated the role of the mTOR pathway as a key upregulated pathway in metastatic EWS. We also identified many of the top genes are collectively targeted by the ubiquitin-protease system to regulate cell death. This led to novel therapeutic work exploring, the use of proteasome inhibitors across a panel Ewing’s sarcoma cell lines and the relationship of these chemotherapeutics with radiation therapy. Ultimately, this work has validated the development of a rigorous and reproducible experimental framework to identify novel pathways driving metastasis in MS cancers. The results pave the way for innovations in both risk stratification, though the use of improved diagnostic tests, and therapeutics, through the development of more targeted molecular therapies.