Abstract
Recent advances in reasoning-enhanced large language models (LLMs) show promise, yet their application in professional medicine, especially the evaluation of their reasoning process, remains underexplored. We present MedR-Bench, a benchmark of 1453 structured patient cases with reference reasoning derived from clinical case reports, spanning 13 body systems and 10 specialties across common and rare diseases. Our evaluation framework covers three stages of care: examination recommendation, diagnostic decision-making, and treatment planning. To assess reasoning quality, we develop the Reasoning Evaluator, an automated scorer of written reasoning along efficiency, factual accuracy, and completeness. We evaluate seven state-of-the-art reasoning LLMs. Here we show that current models exceed 85% accuracy on simple diagnostic tasks when sufficient examination results are available, but performance drops on examination recommendation and treatment planning. Reasoning is generally factual, yet critical steps are often missing. Open-source models are closing the gap with proprietary systems, highlighting potential for more accessible, equitable clinical AI.