Background Coronary artery calcium scoring (CAC) is an excellent non-invasive method to evaluate coronary atherosclerotic burden. To better predict the risk of future events in an individual, their absolute CAC score is compared to an age- and gender-matched cohort in order to assign a percentile rank. However, it is unknown whether absolute CAC or percentile rank is better in predicting obstructive coronary artery disease (CAD). We hypothesized that absolute CAC is superior to percentile rank in predicting obstructive CAD. Methods 210 consecutive patients referred to our institution for CAC and coronary artery computed tomography angiography (CTA) were included. CAC scores were expressed as Agatston score; percentile rank as published by the Multi-Ethnic Study of Atherosclerosis. Coronary artery stenoses were graded semi-quantitatively. Receiver operating characteristics curves (ROC) were used to assess the performance of CAC to predict obstructive CAD. Results In the overall group, the area under the curve (AUC) was significantly greater for absolute CAC compared to MESA percentile rank in predicting obstructive CAD (0.80 vs. 0.72, P = 0.006). Subgroup analysis revealed similar findings: AUC for absolute CAC was greater than for MESA percentile rank in males (0.82 vs. 0.71, P = 0.008), females (0.78 vs. 0.72, P = 0.085), symptomatic patients (0.78 vs. 0.72, P = 0.067) and in asymptomatic subjects (0.89 vs. 0.74, P = 0.05). Conclusion Absolute CAC is superior to MESA percentile rank in predicting obstructive CAD. This finding was seen in both symptomatic and asymptomatic patients as well as in males and females.