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Motivation: Disease diagnosis oriented dialogue system models the interactive consultation procedure as Markov Decision Process and reinforcement learning algorithms are used to solve the problem. Existing approaches usually employ a flat policy structure that treat all symptoms and diseases equally for action making. This strategy works well in the simple scenario when the action space is small, however, its efficiency will be challenged in the real environment. Inspired by the offline consultation process, we propose to integrate a hierarchical policy structure of two levels into the dialogue systemfor policy learning. The high-level policy consists of amastermodel that is responsible for triggering a low-levelmodel, the lowlevel policy consists of several symptom checkers and a disease classifier. The proposed policy structure is capable to deal with diagnosis problem including large number of diseases and symptoms. Results: Experimental results on three real-world datasets and a synthetic dataset demonstrate that our hierarchical framework achieves higher accuracy and symptom recall in disease diagnosis compared with existing systems. We construct a benchmark including datasets and implementation of existing algorithms to encourage follow-up researches. Availability: The code and data is available from https://github.com/FudanDISC/DISCOpen-MedBox-DialoDiagnosis Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.