Beneath the Antarctic ice sheets there is an aquatic subglacial ecosystem which consists of a complex network of subglacial lakes and interconnecting water courses. The possibility of microbial life surviving in extreme environments has led to the direct sampling of several subglacial lakes. To ensure the validity and integrity of results, rigorous risk management planning and clean methods of sampling must be adopted to prevent the risk of contaminating both the samples and the natural biodiversity of these isolated ecosystems. Following the Code of Conduct for the environmental stewardship of these environments and the application of clean sampling methods such as hot water drilling are the safest option currently available. All current and future research projects should be undertaken only after undertaking a detailed risk analysis, and research operators should practise their methodologies on small scale lakes so that they can learn from this baseline information and thus reduce the environmental impacts of their exploration methods.