Purpose: A review of 228 cost-effectiveness analyses found that 77 percent did not incorporate community-based preferences, and 33 percent used arbitrary expert or author judgment. Availability of nationally representative preference-based scores may encourage the understanding of and appropriate use of utilities in cost-effectiveness research. Methods: The current research examines the Health Utility Index Mark II and III scores associated with several common chronic conditions in a nationally representative population in the U.S. using data from the US Valuation of the EQ-5D Health States Study. After controlling for sociodemographic characteristics and other confounders, the marginal decrements in HUI2 and HUI3 scores for each condition are reported and compared. The ceiling effect of the HUI2, HUI3 and EQ-5D is also compared. To address censoring, the results of multivariate regression analyses using OLS, Tobit and censored least absolute deviations (CLAD) are employed and compared. Results: The EQ-5D displays a significantly greater degree of censoring than the HUI2 or HUI3. Marginal decrements in preference scores varied by condition, sociodemographic characteristic, instrument and econometric approach. HUI2/3 scores for older age categories were lower than younger categories, female scores were lower than males, certain racial groups had lower scores than others, and scores were higher for individuals with higher education and income levels. Conclusion: There are differences in the degree of censoring between the EQ-5D and the HUI2/3. The econometric approach chosen has a significant impact on the magnitude of estimates. The chronic condition scores reported in this research are nationally representative and may provide insight to how preferences differ across conditions, econometric methods and instruments used.