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Objective: To investigate and analyze the distribution of 121 diseases of China's First List of Rare Diseases based on hospitalized patients of tertiary hospitals and to explore the current situation of rare diseases in China. Methods: Based on previous data of study from Beijing Society of Rare Diseases, a comparison between China's First List of Rare Diseases and the survey list from the pre-study was performed. Descriptive analysis was carried out on the current situation of rare diseases on hospitalizations in 96 tertiary hospitals from year of 2014 to 2015. Results: Nineteen out of 121 diseases on China's First List of Rare Diseases were not included in the rare diseases survey list of Beijing Society of Rare Diseases. The total number of other 102 rare disease cases was 54 468, accounting for 0.35% of the inpatients during the same period. The top ten most and least cases with rare disease were demonstrated in this study. The number of the top ten most cases was 37 977, accounting for 0.25% of the inpatients during the same period. The number of the top ten least cases was 24, accounting for 0.000 16% of the inpatients during the same period. The top most five types of rare diseases counted on the provinces and municipalities were Beijing, Hunan, Shanghai, Shandong and Guangdong. The top five most cases of rare diseases counted on the provinces and municipalities were Beijing, Shanghai, Guangdong, Shandong and Hubei. The age distribution showed that the cases with rare diseases aged 25-64 years accounted for 45.8%, and the cases in children aged 0-14 accounted for 28.6%. The top ten readmission rate ranged from 28.42% to 64.88%. Conclusions: This study preliminarily investigates the number, type, province and municipality distribution, age distribution, and readmission rate of 121 rare diseases from China's First List of Rare Diseases in the hospitalized patients of tertiary hospitals, which provides important data for registration study, medical and drug policy making and other relevant work on rare diseases in China in the future.