Although substantial intersystem variability has been shown among several commercially available quantitative angiographic (QA) analysis algorithms, no previous study has compared the angiographic findings using 2 different QA systems performed at the same central angiographic laboratory. The purpose of this study was to compare the early and late QA results obtained with the CMS (MEDIS) and ARTREK (ImageComm) QA systems in the Balloon versus Optimal Atherectomy Trial. Directional atherectomy (n = 496) or balloon angioplasty (n = 490) was performed in 986 patients; late QA follow-up was available in 767 patients (77.7%). QA analysis was performed by 2 independent observers using the CMS and ARTREK systems. Correlation between the 2 QA systems for baseline measurements was good (Pearson's R = 0.78), although the CMS system resulted in larger baseline reference diameter (RD) (3.22 +/- 0.45 vs 3.07 +/- 0.40 mm; p <0.0001) and baseline minimal lumen diameters (MLD) (1.05 +/- 0.35 vs 0.92 +/- 0.32; mm p <0.0001) than the ARTREK system. The final and follow-up RD (+0.17 and +0.11 mm, respectively) were also larger using the CMS system. In contrast, the final and follow-up measurements of MLD and percent diameter stenosis were not significantly different using the 2 QA systems. The QA system did not affect the ability to detect a difference in restenosis rates (>50% follow-up diameter stenosis) between the 2 treatment groups (CMS, directional atherectomy [31.8%]; balloon angioplasty [40.5%]; p = 0.013 and ARTREK, directional atherectomy [33.9%], balloon angioplasty [41.3%]; p = 0.036). Only lesion irregularity contributed to the difference in baseline measurements of MLD and percent diameter stenosis. We conclude that important differences in measurements of RD, baseline MLD, and percent diameter stenosis were noted using the CMS and ARTREK systems. Both systems, however, were able to detect a treatment benefit associated with directional atherectomy in BOAT. The comparability of other angiographic systems will require similar evaluation in other studies.