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International reporting of epidemiological surveys of spinal muscular atrophy (SMA) in Japan has been limited to Shikoku, despite the epidemiology of the disease in countries worldwide becoming clearer. Treatments of 5q-SMA have been developed, and epidemiological studies are needed. This study aimed to conduct a nationwide epidemiological survey of SMA in Japan to clarify the actual situation of SMA in Japan. Patients with all clinical types of SMA, including neonates and adults, were selected from 1,005 medical facilities in Japan. As of December 2017, the actual number of reported patients with SMA was 658 and the genetic testing rate was 79.5%. The estimated number of patients was 1,478 (95% confidence interval (CI), 1,122–1,834), with a prevalence of 1.17 (95%CI, 0.89–1.45) per 100,000 people and an incidence of 0.51 (95%CI, 0.32–0.71) per 10,000 live births. Incidence rates of 5q-SMA by clinical type were 0.27 (95%CI, 0.17–0.38) and 0.08 (95%CI, 0.04–0.11) per 10,000 live births for type 1 and 2, respectively, in cases with a definitive diagnosis by genetic testing. We found that 363 cases (82.7%) occurred less than 2 years and 88 (20.0%) occurred age of 2 months old or under. This study clarifies the prevalence and incidence of SMA in Japan. As infantile onset accounts for most cases of SMA, newborn screening and subsequent treatment are important to save lives. [ABSTRACT FROM AUTHOR]