This book constitutes the refereed joint proceedings of the Third International Workshop on Deep Learning in Medical Image Analysis, DLMIA 2017, and the 6th International Workshop on Multimodal Learning for Clinical Decision Support, ML-CDS 2017, held in conjunction with the 20th International Conference on Medical Imaging and Computer-Assisted Intervention, MICCAI 2017, in Quebec City, QC, Canada, in September 2017. The 38 full papers presented at DLMIA 2017 and the 5 full papers presented at ML-CDS 2017 were carefully reviewed and selected. The DLMIA papers focus on the design and use of deep learning methods in medical imaging. The ML-CDS papers discuss new techniques of multimodal mining/retrieval and their use in clinical decision support.