Background: The purpose of the study is to investigate the epidemiology and associated medical expenses of motor neuron diseases (MND) in Taiwan. Methods: Data from the National Health Insurance Research Database, involving diagnoses of MND and Certificates of Serious Accidents and Diseases, were retrieved from January 2000 to December 2005. Age- and sex-specific incidences of MND were estimated by dividing the incidence number by population data obtained from the Department of Statistics, Ministry of the Interior. Results: In total, 1,554 patients with MND were identified. The average yearly incidence was 1.05 per 100,000 people. The male to female ratio was 1.51. The incidence rate, which was 1.25 in men and 0.84 in women, tended to increase with age, and peaked in the ranges of 65–69 years in men and 70–74 years in women. The expenses of the medical services associated with MND increased year by year, except for a sudden drop in inpatient expenses in 2005. Conclusions: The incidence of MND in Taiwan was 1.05 per 100,000/year, which was lower than that of Caucasians. The incidence had moderate male predominance and increased with age. With an aging population, case numbers and medical expenses associated with these diseases are expected to rise in future decades.