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Background Central venous thrombosis is a serious and life-threatening complication in hemodialysis (HD) patients with an indwelling catheter. The present study aimed to investigate the prevalence and characteristics of thrombosis of the superior vena cava and auxiliary branches in Chinese HD patients with an indwelling intal jugular venous catheter and to explore its risk factors.Methods Fifty-four patients on maintenance hemodialysis (MHD) with an indwelling catheter were enrolled in this cross-sectional study. The thrombosis of the intal jugular vein, subclavical vein, brachiocephalic vein and superior vena cava was assessed by vascular ultrasound. Collected were data on age, gender, ultrafiltration volume, Kt/V, blood pressure, levels of hemoglobin, serum albumin, lipid, calcium, and phosphorus, and parathyroid hormone.Results The patients were given short- or long-term double lumen central venous catheters. Among them, 42 patients had the catheter placed into the right intal jugular vein, and 12 patients into the left intal jugular vein. Different degrees of central venous thrombosis were found in 33 patients (61.1%). The prevalence of thrombosis in the jugular vein, brachiocephalic vein, subclavical vein and superior vena cava was 61.1% (33/54), 44.4% (24/54), 16.7% (9/54) and 5.6% (3/54), respectively. Among the 33 HD patients with central venous thrombosis, the percentages for one, two, three and four affected veins were 27.3% (9/33), 45.4% (15/33), 18.2% (6/33) and 9.1% (3/33), respectively. Twelve (12/33, 36.4%) of the 33 HD patients with central venous thrombosis had clinical symptoms. Nine patients (27.3%) had edema of the upper extremity and 3 (9.1%) had new-onset symptoms of pulmonary embolism such as cough, chest distress and short breath. The incidences of diabetes mellitus and malignant tumor and levels of lipoprotein a and homocysteic acid were significantly higher in the HD patients with central venous thrombosis than in those without central venous thrombosis. Logistic regressive analysis revealed that high level of homocysteic acid was the important risk factor for central venous thrombosis in HD patients with indwelling catheterization of the intal jugular vein.Conclusions The prevalence of central venous thrombosis in Chinese HD patients with indwelling catheterization of the intal jugular vein is quite high, especially in those patients with diabetes mellitus, malignant tumor, high levels of serum lipoprotein and homocysteic acid. Its clinical symptoms are insidious but dangerous. High level of homocysteic acid may be the important risk factor for central venous thrombosis in Chinese HD patients with indwelling catheterization of the intal jugular vein.