During the past few years, differential diagnosis of soft tissue tumours has improved due to novel molecular diagnostic tools. Besides a better differentiation between different tumour entities the recognition of specific molecular aberrations may also help to identify novel therapeutic targets. One of the most promising examples of effective molecularly driven treatment is the gastrointestinal stromal tumour. Shortly after the detection of gain-of-function mutations in the type III receptor tyrosine kinases KIT and PDGFRα a targeted treatment with the tyrosine kinase inhibitor imatinib was introduced and became the gold standard in advanced GIST disease. The success of this therapy with response rates of >80% stable disease and partial remission is still unmatched. Since then, many groups aim to identify other potential molecular targets. Genomic and proteomic signatures may pinpoint potential areas of interest for diagnostic tools, prediction of clinical outcome and potential response to therapeutic targets. This article gives an overview of the most important genomic aberrations in sarcomas, their differential diagnosis and the relevance of molecular biology for treatment strategies.