The factors that determine the anatomical variations of the coronary venous system (CVS) are poorly understood. The objective of this study was to evaluate the anatomical variations of the CVS in patients with coronary artery calcification. 196 patients underwent non-contrast CT and coronary CT angiography using 256-slice CT. All subjects were divided into four groups based on their coronary artery calcium score (CACS): 50 patients with CACS = 0 Agatston unit (AU), 52 patients with CACS = 1–100 AU, 44 patients with CACS = 101–400 AU, and 50 patients with CACS > 400 AU. The presence of the following cardiac veins was evaluated: the coronary sinus (CS), great cardiac vein (GCV), posterior interventricular vein (PIV), posterior vein of the left ventricle (PVLV), left marginal vein (LMV), anterior interventricular vein (AIV), and small cardiac vein (SCV). Vessel diameters were also measured. We found that the CS, GCV, PIV, and AIV were visualized in all patients, whereas the PVLV and LMV were identified in a certain proportion of patients: 98% and 96% in the CACS = 0 AU group, 100% and 78.8% in the CACS = 1–100 AU group, 93.2% and 77.3% in the CACS = 101–400 AU group, and 98% and 78% in the CACS > 400 AU group, respectively. The LMV was less often identified in the last three groups than in the first group (p < 0.05). The frequency of having either one PVLV or LMV was higher in the last three groups than in the first group (p < 0.05). No significant differences in vessel diameters were observed between the groups. It was concluded that patients with coronary artery calcification were less likely to have the LMV, which might hamper the left ventricular lead implantation in cardiac resynchronization therapy.