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