•Reiwa First Year East Japan typhoon of 2019 caused great damage in Nagano city.•First report on effect of flood on cardiovascular and cerebrovascular diseases.•Total number of cases did not increase significantly compared with previous 2 years.•Cases of heart failure, acute myocardial infarction, unstable angina increased.•Guidelines should be implemented to deal with expected rise in such cases after floods. The Reiwa First Year East Japan Typhoon of 2019 caused a torrential flood in Japan. In Nagano City, a large area was flooded due to the collapse of the Chikuma River embankment. After large-scale disasters, an increase in cardiovascular and cerebrovascular events has been reported on account of the stressful conditions. However, few reports of disaster-related diseases associated with flood damage have been described. Thus, our aim was to elucidate the effect of floods on the incidences of cardiovascular and cerebrovascular diseases in Nagano City. The Shinshu Assessment of Flood Disaster Cardiovascular Events (SAVE) trial enrolled 2,426 patients admitted for cardiovascular or cerebrovascular diseases at all five hospitals with an emergency department in Nagano City from October 1 to December 31 in the years 2017, 2018, and 2019. The occurrence of these diseases was calculated in every 2 weeks and the findings of 2019 (year of the flood) were compared with those of 2017 and 2018. Cardiovascular and cerebrovascular diseases significantly increased during the 2 weeks immediately after the flood disaster (149 in 2019 vs average of 116.5 in the previous 2 years, p < 0.05). Unstable angina cases significantly increased 1.5–2 months after the flood disaster, and cerebral hemorrhage cases significantly increased in the 2 weeks after the flood disaster. Cardiovascular and cerebrovascular events increased significantly during the 2 weeks immediately after the large-scale flood disaster caused by the Reiwa First Year East Japan typhoon. Because of the increasing frequency of flood disasters, it is necessary to predict the occurrences of cardiovascular and cerebrovascular diseases and to implement guidelines for their appropriate and timely management. Display omitted