Left atrial enlargement is an independent risk factor for ischemic stroke in patients with atrial fibrillation. Little is known regarding the association between nighttime blood pressure variability and left atrial enlargement in patients with atrial fibrillation and preserved ejection fraction. The study population consisted of 140 consecutive patients with atrial fibrillation (mean age 64 ± 10 years) with preserved ejection fraction (≥50%). Nighttime blood pressure was measured at hourly intervals, using a home blood pressure monitoring device. Nighttime blood pressure variability was expressed as the standard deviation of all readings. Left atrial volume index was measured using the modified Simpson's biplane method with transthoracic echocardiography. Multiple regression analysis indicated that nighttime mean systolic/diastolic blood pressure and its variability remained independently associated with left atrial enlargement after adjustment for age, sex, anti-hypertensive medication class, and left ventricular mass index (P < 0.01). When patients were divided into four groups according to nighttime blood pressure and its variability, the group with higher nighttime blood pressure and its variability had significantly larger left atrial volume than the group with lower nighttime blood pressure and its variability (46.6 ml/m2 vs. 35.0 ml/m2, P < 0.0001). Higher nighttime blood pressure and its variability are associated with left atrial enlargement. The combination of nighttime blood pressure and its variability has additional predictive value for left atrial enlargement. Intensive intervention for these high-risk patients may avoid or delay progression of left atrial enlargement and reduce the risk of stroke.