Studies of animal behavior in remote polar regions are essential to understand ecologic change, yet they require significant human and logistic resources. Behavioral data are mostly gathered by tagging single animals, such as penguins and whales. While tagging delivers high-accuracy data for single animals, it cannot be used to study collective behavior in social species due to high costs and the often time-consuming or disturbing tagging process. We present an alternative approach to study animal behavior using automated, remotely operated and energetically independent image acquisition systems. We developed a land-based system for studying penguins, and a sea-based system to study whales. The sea-based system employs a rotating infrared camera (5 rev/s, 360°) for the automatic detection of whales within a radius of up to 3 nautical miles during day and night, and a high-resolution CCD camera equipped with a telephoto lens. Upon detection of a whale in the thermal image, the CCD-camera is automatically pointed at the respective location, and triggered to acquire photos at 5 Hz, allowing species identification up to several miles distance The imaging system is mounted on an active tilt stage to counteract ship movements in heavy seas, which allows to calculate absolute whale positions with an accuracy of ~10%. From the trajectory of an individual whale, likely areas of subsequent surfacing positions are estimated, providing proactive tracing of the whale, which improves the likelyhood of capturing it on photo and and its identification. Automatic whale detection and identification data may then be used to conduct autonomous line transect surveys throughout the cruise. Continuous automatic whale detections during recent expeditions contibuted significantly to the amount of data available for density calculations and habitat suitability modeling. We will present data from three expeditions on RV Polarstern during the years 2009-2011, including several tens of ship-whale encounters. The system will be used during two more expeditions in early 2012, for automatic marine mammal detection, localization and identification purposes. Our land-based system employed a simpler image acquisition and automated analysis technology and was first used to study the collective behavior of Emperor penguins during huddling. The system is capable of simultaneously tracking the positions of more than 1400 huddling emperor penguins. The trajectories revealed that Emperor penguins move collectively in a highly coordinated manner to ensure mobility while at the same time keeping the huddle tightly packed. Every 30–60 seconds, all penguins make small steps, which travel as a wave through the entire huddle. Over time, these small movements lead to large-scale reorganization of the huddle. Moreover, from the high-resolution images is it possible to obtain a precise count of the penguin colony, and to obtain morphometric data from individual penguins to monitor their nutritional state. Thus far, we built five observatories that are currently being shipped to an Adélie penguin (Adélie Land), King penguin (Crozet Island) and Emperor penguin (Atka Bay, Adélie Land) colony, respectively. All three observatories are designed for year-round operations.