Despite the higher mortality rates in patients with Down syndrome compared with the general Japanese population, the life span has dramatically increased in Japan and other countries. We aimed to clarify recent causes of death in patients with Down syndrome in Japan. We calculated proportionate mortality and standardized mortality odds ratios (SMORs) among all deaths registered with Down syndrome as the cause of death (ICD-10 code, Q90) in the Japanese National Death Registry Database in 2014-2016. In the study period, 762 in patients with Down syndrome died. The main causes of death were pneumonia/respiratory infections (20.5%), congenital malformations of the circulatory system (11.2%), other diseases of the circulatory system (9.2%), and aspiration pneumonia (8.4%). The SMORs (95% confidence intervals) were higher for natural death, defined as death of an elderly person with no other cause of death to be mentioned (55.73 [36.92-84.12]), early-onset Alzheimer's disease, defined as Alzheimer's disease with onset <65 years of age (29.36 [16.44-52.44]), aspiration pneumonia (18.33 [14.03-23.96]), pneumonia/ respiratory infections (8.11 [6.76-9.73]), congenital malformations of the circulatory system (8.07 [5.98-10.88]), and leukemia/lymphoma (2.16 [1.55-2.99]) but lower for malignant solid tumors (0.04 [0.02-0.06]) in patients with Down syndrome. Patients with Down syndrome had the greatest relative risk of dying from natural death, early-onset Alzheimer's disease, and respiratory illnesses, highlighting the need for appropriate medical, health, and welfare services.