Objectives To determine recent trends in mutation patterns in the WRN gene, which cause Werner syndrome ( WS ), a rare, inheritable progeroid syndrome in Japan. Design Retrospective cohort. Setting Longitudinal survey of WS and literature search for case reports. Participants Individuals whose genetic testing their facilities had requested between 2009 and October 2016 (N = 67). Measurements A nationwide epidemiological study was conducted from 2009 to 2011 to improve understanding of the pathology of WS and develop therapeutic guidelines. Since 2009, Chiba University Hospital consecutively evaluated the WRN gene in 67 individuals throughout Japan who had requested genetic testing. A literature search was also conducted for case reports on Japanese WS reported since 1997. Results A definitive diagnosis of WS was confirmed genetically in 50 of 67 participants. Through the literature search, 16 individuals diagnosed genetically with WS were identified. Of these 66 individuals with WS , 42 were homozygous for a WRN mutation, and 21 were compound heterozygotes. One novel mutant allele was identified in an individual with the compound heterozygous genotype. The proportion of compound heterozygotes (31.8%) was significantly greater than reported previously (14.2%), indicating that the incidence of consanguineous marriage of parents has decreased. Conclusion The increased frequency of individuals with WS with the compound heterozygous genotype is a recent trend in Japan. A long‐term follow‐up study on WRN homozygotes and compound heterozygotes will allow the relationship between WRN genotype and clinical severity of WS to be evaluated in the future.