Age-related macular degeneration (AMD) is the leading cause of blindness in the Western world. In this work, the non-invasive imaging technique spectral domain optical coherence tomography (SD-OCT) is used to acquire retinal images, which are then analyzed using deep learning techniques. The authors trained a convolutional neural network (CNN) using 1300 SD-OCT scans annotated by trained experts for the presence of different biomarkers associated with AMD. The CNN was able to accurately segment these biomarkers and the performance was further enhanced through transfer learning with weights from a separate classifier, trained on a large external public OCT dataset to distinguish between different types of AMD. Our model is able to accurately detect and segment AMD biomarkers in OCT scans, which suggests that it could be useful for prioritizing patients and reducing ophthalmologists’ workloads.