The EQ-5D is a widely used preference-based instrument to measure health-related quality of life. Some methodological drawbacks of its three-level version (EQ-5D-3L) prompted development of a new format (EQ-5D-5L). There is no clear evidence that the new format outperforms the standard version. The objective of this study was to make a head-to-head comparison of the EQ-5D-3L and EQ-5D-5L in a discrete choice model setting giving special attention to the consistency and logical ordering of coefficients for the attribute levels and to the differences in health-state values. Using efficient designs, 240 pairs of EQ-5D-3L health states and 240 pairs of EQ-5D-5L health states were generated in a pairwise choice format. The study included 3698 Dutch general population respondents, analyzed their responses using a conditional logit model, and compared the values elicited by EQ-5D-3L and EQ-5D-5L for different health states. No inconsistencies or illogical ordering of level coefficients were observed in either version. The proportion of severe health states with low values was higher in the EQ-5D-5L than in the EQ-5D-3L, and the proportion of mild/moderate states was lower in the EQ-5D-5L than in the EQ-5D-3L. Moreover, differences were observed in the relative weights of the attributes. Overall distribution of health-state values derived from a large representative sample using the same measurement framework for both versions showed differences between the EQ-5D-3L and EQ-5D-5L. However, even small differences in the phrasing (language) of the descriptive system or in the valuation protocol can produce differences in values between these two versions.