BACKGROUND AND PURPOSE: Thromboembolism in paroxysmal atrial fibrillation (AF) has often been attributed to occult AF. We hypothesized that the surface ECG may not always reflect left atrial appendage (LAA) mechanical function. METHODS: Transesophageal echocardiographic images from 201 consecutive patients undergoing transesophageal echocardiography by a single operator were reviewed. LAA pulse wave Doppler phenotype, ECG rhythm, and mitral valve motion for rhythm of the body of the left atrium and the electronic medical record were reviewed by 3 blinded, independent observers. RESULTS: Of 201 patients (63.4+/-15 years; 61% men) undergoing transesophageal echocardiography, 15 (7.5%) demonstrated LA-LAA discordance including 7 (3.5%) with a sinus rhythm ECG/mitral valve motion and an AF LAA pulse wave Doppler phenotype. Of 24 patients with a clinical history of AF but sinus rhythm ECG, 25% demonstrated a discordant AF LAA pulse wave Doppler phenotype. Compared with concordant AF, the AF discordant group had greater CHA2DS2-VASc (CHADS2, vascular disease, age, sex category; P=0.008) and lower LAA ejection velocity (P=0.02). CONCLUSIONS: A quarter of patients with paroxysmal AF demonstrate a prothrombotic AF LAA pulse wave Doppler phenotype, despite concurrent sinus rhythm ECG. These findings provide a novel explanation for ongoing thromboembolism in the paroxysmal AF population, despite apparent ECG maintenance of sinus rhythm.