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Although atrial septal aneurysm (ASA) is frequently combined with patent foramen ovale and associated with cryptogenic stroke (CS), a pathophysiologic correlation between CS and ASA alone has not been fully elucidated. The aims of this study were to assess transport functions of the left atrium (LA) and left atrial appendage (LAA), and to evaluate their relationship in CS subjects with ASA alone.This study consisted of 38 CS subjects with ASA alone and 38 matched controls. Transthoracic echocardiography including tissue Doppler imaging was performed in all subjects and transesophageal echocardiography was conducted in CS subjects to assess LAA emptying velocity (LAAev). We also measured soluble P- and E-selectin, interleukin-6 (IL-6), and high-sensitivity C-reactive protein (hs-CRP) as indices of prothrombogenic and proinflammatory activity. Although there were no differences in left ventricular functions and baseline characteristics between the two groups, CS subjects had significantly larger LA volume and lower LA active pump function compared with controls. LAAev was significantly correlated with LA active function. CS subjects had significantly higher E-selectin (P = 0.046), IL-6 (P = 0.040), and hs-CRP (P = 0.001) compared with controls.Compared with controls, LA active pump function was significantly depressed and closely correlated with LAAev in CS subjects with ASA alone. Moreover, plasma levels of E-selectin, IL-6, and hs-CRP were significantly higher in CS subjects with ASA alone. These findings suggest that impaired LA and LAA functions are a crucial pathophysiologic mechanism for ischaemic stroke in subjects with ASA alone.