Quality-adjusted life-years (QALYs) use preference-based measurements of health-related quality-of-life (HRQOL) to provide an assessment of the overall burden of disease using a single number. This study estimated QALYs lost contributed by smoking and obesity for U.S. adults from 1993 to 2008. Population HRQOL data were from the 1993-2008 Behavioral Risk Factor Surveillance System. The QALYs lost contributed by a risk factor is the sum of QALYs lost due to morbidity in the current year and future QALYs lost in expected life-years due to premature deaths (mortality). Premature deaths were estimated from the National Health Interview Survey Linked Mortality Files and mortality statistics. From 1993 to 2008, the proportion of smokers among U.S. adults declined 18.5% whereas the proportion of obese people increased 85%. The smoking-related QALYs lost were relatively stable at 0.0438 QALYs lost per population. In 1993 the QALYs lost were much smaller for obesity compared to smoking, with obesity contributing about 0.0204 QALYs lost. However, as a result of the increasing prevalence of obesity, the contribution of obesity-related QALYs lost increased consistently and had increased by 127% in 2008 when obesity resulted in 0.0464 QALYs lost, slightly more than smoking did. Smoking had a bigger impact on mortality than morbidity, whereas obesity had a bigger impact on morbidity than mortality. This study estimated the overall burden of smoking and obesity over time and results indicate that because of the marked increase in the proportion of obese people, obesity has become an equal, if not greater, contributor to the burden of disease than smoking. Such data are essential in setting targets for reducing modifiable health risks and eliminating health disparities.