BackgroundRare diseases, though individually uncommon, collectively affect a significant portion of the population. However, their epidemiology in China remains underexplored. A population-based rare disease registry comprising 14.31 million individuals was conducted between 2012 and 2023 by the Beijing Municipal Health Big Data and Policy Research Center. Rare disease cases were identified via ICD-10 codes mapped to China's national rare disease lists (2018 and 2023) and international databases. Age-standardized incidence rates (ASIR) were calculated per 100,000 person-years with 95% confidence intervals.ResultsOur analysis identified 12,371 rare disease cases, with the overall ASIR increasing from 6.109 in 2012 to 7.394 in 2023. Rare neurologic diseases accounted for 52.12% of cases, followed by systemic and rheumatologic diseases (16.89%) and rare neoplastic diseases (9.99%). The most frequently diagnosed rare diseases included generalized myasthenia gravis, ANCA-associated vasculitis, and malignant melanoma. Significant sex-based differences were observed, with female patients more affected by systemic and rheumatologic conditions, while male patients showed a higher incidence of respiratory disorders. Pediatric patients predominantly presented with inborn errors of metabolism and rare immune diseases. Comparisons with global data revealed notable disparities, such as a higher prevalence of Wilson's disease and a lower incidence of amyotrophic lateral sclerosis (ALS) in China.ConclusionsThis study represents the first large-scale, population-based analysis of rare diseases in China, revealing distinct epidemiological patterns. These findings underscore the critical need for healthcare policies that address the unique challenges posed by rare diseases in China.