The three-volume set LNCS 15916,15917 & 15918 constitutes the refereed proceedings of the 29th Annual Conference on Medical Image Understanding and Analysis, MIUA 2025, held in Leeds, UK, during July 15–17, 2025. The 67 revised full papers presented in these proceedings were carefully reviewed and selected from 99 submissions. The papers are organized in the following topical sections:Part I: Frontiers in Computational Pathology; and Image Synthesis and Generative Artificial Intelligence. Part II: Image-guided Diagnosis; and Image-guided Intervention. Part III: Medical Image Segmentation; and Retinal and Vascular Image Analysis.