Medicare Advantage (MA) has grown rapidly since the Affordable Care Act; nearly one-third of Medicare beneficiaries now choose MA. An assessment of the comparative value of the 2 options is confounded by an apparent selection bias favoring MA, as reflected in mortality differences. Previous assessments have been hampered by lack of access to claims diagnosis data for the MA population. An indirect comparison of mortality as an outcome variable was conducted by modeling mortality on a traditional fee-for-service (FFS) Medicare data set, applying the model to an MA data set, and then evaluating the ratio of actual-to-predicted mortality in the MA data set. The mortality model adjusted for clinical conditions and demographic factors. Model development considered the effect of potentially greater coding intensity in the MA population. Further analysis calculated ratios for subpopulations. Predicted, risk-adjusted mortality was lower in the MA population than in FFS Medicare. However, the ratio of actual-to-predicted mortality (0.80) suggested that the individuals in the MA data set were less likely to die than would be predicted had those individuals been enrolled in FFS Medicare. Differences between actual and predicted mortality were particularly pronounced in low income (dual eligibility), nonwhite race, high morbidity, and Health Maintenance Organization (HMO) subgroups. After controlling for baseline clinical risk as represented by claims diagnosis data, mortality differences favoring MA over FFS Medicare persisted, particularly in vulnerable subgroups and HMO plans. These findings suggest that differences in morbidity do not fully explain differences in mortality between the 2 programs.