Objective: To compare the clinical quality of care between Medicare fee-for-service (FFS) and Medicare Advantage (MA) programs. Methods: We compared 11 Healthcare Effectiveness Data and Information Set (HEDIS) quality measures nationwide for MA managed care plans and the FFS program in 2006 and 2007. We adjusted FFS measures to match the geographic distribution of MA. Results: Medicare Advantage plans scored substantially better (4-16 percentage points; median, 7.8 percentage points) on 8 measures, slightly better (1.5 percentage points) on 1 measure, and worse than FFS (2-5 percentage points; median, 4.1 percentage points) on 2 measures. The 8 measures on which MA scored substantially better were well established in the HEDIS measure set (introduced in the 1990s), whereas the other 3 were all newer (introduced in 2004-2005 data). Data and program differences complicated the comparison, but it is unlikely that they were large enough to explain the sizable MA-FFS gaps observed. Conclusions: Quality measures showed large, though mixed, differences between MA and FFS. The dichotomy between older and newer measures in MA suggests a learning effect, with plans improving measurement and quality over time as measures become more familiar. (Am J Manag Care. 2070;16(71):841-848)