Different to semantic segmentation, instance segmentation assigns unique labels to each individual instance of the same class. In this work, we propose a novel recurrent fully convolutional network architecture for tracking such instance segmentations over time.Thenetwork architecture incorporates convolutional gated recurrent units (ConvGRU) into a stackedhourglass network toutilize temporal video information.Furthermore, we train the network with a novel embedding loss based on cosine similarities, such that the network predicts unique embeddings for every instance throughout videos. Afterwards, these embeddings are clustered among subsequent video frames to create the final tracked instance segmentations. We evaluate the recurrent hourglass network by segmenting left ventricles in MR videos of the heart, where it outperforms a network that does not incorporate video information. Furthermore, we show applicability of the cosine embedding loss for segmenting leaf instances on still images of plants. Finally, we evaluate the framework for instance segmentation and tracking on six datasets of the ISBI celltracking challenge,where it shows state-of-the-art performance.