This book constitutes the refereed proceedings of the Third International Workshop on Connectomics in NeuroImaging, CNI 2019, held in conjunction with MICCAI 2019 in Shenzhen, China, in October 2019.The 13 full papers presented were carefully reviewed and selected from 14 submissions. The papers deal with new advancements in network construction, analysis, and visualization techniques in connectomics and their use in clinical diagnosis and group comparison studies as well as in various neuroimaging applications.