The Southern Ocean provides the principal connection between the Earth’s ocean basins and between the upper and lower layers of the global ocean circulation. As a result, the Southern Ocean strongly influences climate patterns and the cycling of carbon and nutrients. Changes in the Southern Ocean therefore have global ramifications. Limited observations suggest the Southern Ocean is indeed changing: the region is warming more rapidly than the global ocean average; salinity changes driven by changes in precipitation and ice melt have been observed in both the upper and abyssal ocean; the uptake of carbon by the Southern Ocean has slowed the rate of atmospheric climate change but caused basin-wide ocean acidification; and Southern Ocean ecosystems are reacting to changes in the physical and chemical environment. However, the short and incomplete nature of existing time series makes the causes and consequences of observed changes difficult to assess. Sustained, multi-disciplinary observations are required to detect, interpret and respond to change. The Southern Ocean Observing System (SOOS) is needed to address six overarching scientific challenges: 1. The role of the Southern Ocean in the planet’s heat and freshwater balance 2. The stability of the Southern Ocean overturning circulation 3. The role of the ocean in the stability of the Antarctic ice sheet and its contribution to sea-level rise 4. The future and consequences of Southern Ocean carbon uptake 5. The future of Antarctic sea ice 6. The impacts of global change on Southern Ocean ecosystems There is an urgent need to increase understanding in each of these areas to inform decision-makers confronted with the challenges of climate change, sea-level rise, ocean acidification, and the sustainable management of marine resources. To deliver this information, sustained observations of the physical, biogeochemical and biological state of the Southern Ocean are critical. The lack of historical observations has slowed progress in understanding the Southern Ocean and its connections to other parts of the Earth system. However, advances in technology and knowledge mean that it is now possible to design and implement a sustained, feasible and cost-effective observing system for this remote environment. Users of the SOOS will include the research community, managers of marine resources, policy makers, local planners, ship operators, Antarctic tourism operators, weather and climate forecasters, and educators. Several international organisations, including the Intergovernmental Oceanographic Commission of UNESCO, the World Meteorological Organisation, the Scientific Committee on Oceanic Research, and the Scientific Committee on Antarctic Research, have noted the compelling need for sustained observations of the Southern Ocean and supported the development of the SOOS. This document outlines the scientific rationale and strategy for the SOOS; identifies the variables to be observed; presents a draft plan for an integrated multi-disciplinary observing system for the Southern Ocean; and identifies the next steps required for implementation.