Persistent left superior vena cava (PLSVC) is one of the most common thoracic venous anomaly and rarely noticed, because it is asymptomatic. However, for nephrologists, it is frequent enough to be encountered while placing hemodialysis catheters through the jugular vein. We report the case of 66-year-old patient with PLSVC presenting intrinsic thrombosis formation 4 h after dialysis catheter placed. Dialysis catheter was placed in the left internal jugular vein without resistance and any complication. PLSVC was detected after dialysis catheter insertion. We decided to remove the catheter, because the patient has other veins in which the catheter can be placed. When it was removed 4 h after catheter placing, thrombus was recognized in the catheter lumen. Transesophageal echocardiography was performed and no thrombus formation was observed in the heart chamber. For patients with PLSVC, if there were other veins in which the catheter can be placed, catheter replacement should be considered.