Explainability of decoder-only clinical large language models: A scoping review

Clinical large language models (LLMs) are increasingly used for documentation, diagnosis, and decision support, but their opaque reasoning can limit clinician trust, regulatory assessment, and safe deployment. Explainability research has expanded rapidly, yet existing reviews largely address traditional machine learning or general-domain LLMs. We conducted a PRISMA-ScR scoping review to map explainability approaches for decoder-only clinical LLMs with over one billion parameters, searching PubMed, Scopus, Web of Science, ACM Digital Library, and arXiv through early 2026. Among 69 included studies, LLM-native generative and interactive methods dominated (58.0%, n = 40), spanning chain-of-thought rationales, retrieval-augmented evidence citation, and agentic decomposition. Intrinsic by-design methods accounted for 24.6% (n = 17); post-hoc XAI methods accounted for 17.4% (n = 12). General medicine was the most represented clinical domain, and diagnosis was the dominant task. Proprietary models were used in 75.4% of studies, yet every mechanistic analysis relied on open-source models, revealing a transparency asymmetry: most deployed models are the least transparent. Although 59.4% of studies quantitatively evaluated explanations, metrics remain non-standardized and rarely assess faithfulness. Local explanations predominated, and no study prospectively evaluated explanations in live clinical workflows. These findings show that clinical LLM explainability has shifted toward fluent generative rationales, but evidence that such explanations reflect model reasoning remains limited. To support trustworthy deployment, we highlight three regulatory priorities: prioritizing explanations that enable independent verification or logic auditing over plausibility-only rationales; preferring inspectable models where regulatory documentation is required; and prospectively validating explanations in clinical workflows before scaling.