Patients with chronic kidney disease (CKD) experiencing atrial arrhythmia are hypothesized to have elevated CHADS₂ and CHA₂DS₂-VASc scores, thereby predisposed to left atrial (LA) thrombus formation and subsequent thromboembolism. We examined possible association of LA thrombogenic milieu (TM) with CKD in patients with nonvalvular atrial fibrillation. A total of 581 patients (181 women; mean age, 67 years) who underwent transesophageal echocardiography were examined. Patients were divided into 4 groups based on the estimated glomerular filtration rate (eGFR) (ml/min/1.73 m²): eGFR ≥90 (n = 29), 60≤ eGFR <90 (n = 329), 30≤ eGFR <60 (n = 209), and eGFR <30 (n = 14). TM was defined as the presence of LA thrombus, dense spontaneous echo contrast, or LA appendage velocity ≤25 cm/s. Of 581 patients, 147 (25%) had TM. The prevalence of TM increased with decreasing eGFR (4%, 18%, 36%, and 86% for each group, p <0.001). Similar trends were observed for some of the clinical and echocardiographic variables including CHA₂DS₂-VASc score and LA size. Multivariate logistic regression analysis revealed that every 10 ml/min/1.73 m² decrement in eGFR was a significant independent correlate of TM (odds ratio 0.80, p = 0.005), along with nonparoxysmal atrial fibrillation (AF) (odds ratio 0.45, p = 0.004), higher CHA₂DS₂-VASc score (odds ratio 1.24, p = 0.012), every 5 ml/m² increment in LA volume index (odds ratio 1.57, p <0.001), and every 10% decrement in left ventricular ejection fraction (odds ratio 0.51, p <0.001). In conclusion, CKD may be a significant risk factor for LA thrombus formation in patients with nonvalvular atrial fibrillation.