The CHADS₂ score predicts the risk of ischaemic stroke in patients with non-valvular atrial fibrillation (NVAF). Most components of the CHADS₂ score are also risk factors of atherosclerosis, and clustering of these risk factors is associated with increased risk of cardiovascular disease, including ischaemic heart disease. The aim of this study was to investigate whether the CHADS₂ score and CHA₂DS₂-VASc score are predictive of fatal ischaemic heart disease as well as fatal ischaemic stroke. Among 5,268 stroke patients admitted between August 1994 and December 2008, 770 stroke patients with NVAF were enroled in this study. The relationship between CHADS₂ score or CHA₂DS₂-VASc score and the fatal ischaemic events was examined using a Cox regression model. During the follow-up period of 1156.0 ± 1205.0 days (median 729.5, interquartile range 179.0-1751.0), 321 patients died (41.7%). The CHADS₂ score or CHA₂DS₂-VASc score was positively correlated with fatal ischaemic heart disease as well as with fatal ischaemic stroke. After adjustment for all potential confounders, the occurrence of fatal ischaemic heart disease was independently associated with CHADS₂ score or CHA₂DS₂-VASc score, and previous history of ischaemic heart disease. The CHADS₂ and CHA₂DS₂-VASc scores provide valuable information for identifying high-risk individuals for fatal ischaemic heart and brain diseases among stroke patients with NVAF.