Coronary calcium screening using electron beam computed tomography (EBCT) is being applied clinically and for research purposes. We compared the accuracy of a specialized image analysis system with the standard proprietary software in the scanner's host computer. Sixty-seven symptomatic patients underwent coronary angiography and EBCT. Tomograms were analyzed using the proprietary software included in the scanner and with a specialized coronary calcium scoring work station. Sensitivities, specificities, and receiver operating characteristic curve areas were calculated for the proprietary software and the specialized system using the angiographic definition of disease of at least one stenosis causing greater than 50% luminal narrowing. There were no significant differences between the proprietary and the specialized software's accuracy. Receiver operating characteristic curve areas were 0.84 and 0.82 for proprietary software, respectively. During a 50 minute analysis session, the average number of studies analyzed were 12.6 +/- 1.7 using the proprietary software and 23.2 +/- 5.7 using the specialized software (P = .02).Image analysis was thus found to be more rapid using the specialized software. The specialized coronary calcium analysis system is as accurate as the proprietary software for scoring EBCT for coronary calcium. The reduction in analysis time makes the specialized system the preferable method.