With a rigorous long-term archival of endoscopic surgeries, vast amounts of video and image data accumulate. Surgeons are not able to spend their valuable time to manually search within endoscopic multimedia databases (EMDBs) or manually maintain links to interesting sections in order to quickly retrieve relevant surgery sections. Enabling the surgeons to quickly access the relevant surgery scenes, we utilize the fact that surgeons record external images additionally to the surgery video and aim to link them to the appropriate video sequence in the EMDB using a query-by-example approach. We propose binary Convolutional Neural Network (CNN) features off-the-shelf and compare them to several baselines: pixel-based comparison (PSNR), image structure comparison (SSIM), hand-crafted global features (CEDD and feature signatures), as well as CNN baselines Histograms of Class Confidences (HoCC) and Neural Codes (NC). For evaluation, we use 5.5 h of endoscopic video material and 69 query images selected by medical experts and compare the performance of the aforementioned image mathing methods in terms of video hit rate and distance to the true playback time stamp (PTS) for correct video predictions. Our evaluation shows that binary CNN features are compact, yet powerful image descriptors for retrieval in the endoscopic imaging domain. They are able to maintain state-of-the-art performance, while providing the benefit of low storage space requirements and hence provide the best compromise.