This paper aims to describe a general demographic picture of patients with rare diseases in Taiwan and particularly focuses on the prevalence of rare diseases over time, age and gender distributions. We analyzed data mainly from the national disability registry from 2002 to 2011 in Taiwan, Republic of China. The results showed that the number of rare diseases increased from 93 to 193 between 2002 and 2011 and that the prevalence of rare diseases increased from 0.02 to 0.74 per 10,000 people in this time period. The gender ratio (male/female) was between 1.02 and 1.13 during this time period, with male cases representing a higher percentage than female cases in the rare disease population. The occurrence of rare diseases was significantly increased in children 3-5 years of age and elementary school children 6-14 years of age. The data also revealed that the occurrence of rare diseases in Taiwan was attributed primarily to pathogenic diseases and secondarily to genetic diseases. To obtain precise epidemiological data on rare diseases for future healthcare planning, this study highlights the importance of the cooperation of healthcare authorities with the social welfare department to strengthen the ability of the public healthcare system to regularly monitor and measure the occurrence of rare diseases in the community. (Contains 3 tables and 3 figures.)