As baleen whales recover from severe exploitation, they are probably subject to a wide variety of threats within the Antarctic marine ecosystem, including directed take. Here we review both the management and current status of Antarctic baleen whales and consider those threats likely to impact on them. Threats range from global problems - marine pollution and climate change - to localized issues including shipping, habitat disturbance, unregulated wildlife tourism and fishery activities. We identify the most pressing anthropogenic threats to baleen whales including scientific whaling and climate change. It is unclear whether current management approaches will be able to effectively encompass all these threats while also accounting both for the differing levels of scientific understanding and for the differing recovery rates of the whale species. For management we recommend the following: 1) incorporation of both ecosystem considerations and the suite of identified threats not limited to direct take, 2) identification of measurable indicators of changes in whales that allow more certainty in monitoring of populations and the environment, and 3) recognition of significant relationships between baleen whales and habitat features to provide information on distribution and use.