The 16-volume set LNCS 15960 - 15975 constitutes the refereed proceedings of the 28th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2025, which took place in Daejeon, South Korea, during September 23&27, 2025.The total of 1027 papers included in the proceedings was carefully reviewed and selected from 3447 submissions. They were organized in topical parts as follows:Part I, LNCS Volume 15960: Multimodal Fusion and Contextual Reasoning in Medical ImagingPart II, LNCS Volume 15961: Surgical Navigation, Scene Understanding, and Video ModelingPart III, LNCS Volume 15962: Learning and Augmented Reality for Surgical and Endoscopic Applications (I)Part IV, LNCS Volume 15963: Learning and Augmented Reality for Surgical and Endoscopic Applications (II)Part V, LNCS Volume 15964: Graph-Based Methods in Medical ImagingPart VI, LNCS Volume 15965: Datasets and Methods for Image Quality EnhancementPart VII, LNCS Volume 15966: Trustworthy and Responsible AI for Medical ImagingPart VIII, LNCS Volume 15967: Multimodal Learning for Diagnosis, Risk Prediction, and Survival AnalysisPart IX, LNCS Volume 15968: Core Techniques in Medical Imaging: Segmentation, Registration, Synthesis, Reconstruction, and Other Emerging Methods (I)Part X, LNCS Volume 15969: Core Techniques in Medical Imaging: Segmentation, Registration, Synthesis, Reconstruction, and Other Emerging Methods (II)Part XI, LNCS Volume 15970: Core Techniques in Medical Imaging: Segmentation, Registration, Synthesis, Reconstruction, and Other Emerging Methods (III)Part XII, LNCS Volume 15971: Core Techniques in Medical Imaging: Segmentation, Registration, Synthesis, Reconstruction, and Other Emerging Methods (IV)Part XIII, LNCS Volume 15972: Adapting Foundation Models for Medical Imaging: LLMs, VLMs, and Cross-Domain Generalization (I)Part XIV, LNCS Volume 15973: Adapting Foundation Models for Medical Imaging: LLMs, VLMs, and Cross-Domain Generalization (II)Part XV, LNCS Volume 15974: Adapting Foundation Models for Medical Imaging: LLMs, VLMs, and Cross-Domain Generalization (III)Part XVI, LNCS Volume 15975: Statistical Techniques in Medical Imaging: Causality, Imputation, Weak Supervision, and Other Methods