BACKGROUND: The SF-6D was derived from the SF-36. A single summary score is obtained allegedly preserving the descriptive richness and sensitivity to change of the SF-36 into utility measurement. We compared the SF-6D and EQ-5D on domain content, scoring distribution, pre-treatment and change scores. METHODS: The SF-6D and the EQ-5D were completed prior to intervention and 1, 3, 6 and 12 months post-intervention in a study enrolling 561 patients with symptomatic coronary stenosis. Patients were randomized to off-pump coronary artery bypass surgery (CABG), standard on-pump CABG, or percutaneous transluminal coronary angioplasty (PTCA). Baseline and change over time scores were compared using parametric and non-parametric tests. RESULTS: The relative contribution of similar domains measuring daily functioning to the utility scores differed substantially. SF-6D focused more on social functioning, while EQ-5D gave more weight to physical functioning. Pain and mental health had similar contributions. The scoring range of the EQ-5D was twice the range of the SF-6D. Before treatment, EQ-5D and SF-6D mean scores appeared similar (0.64 versus 0.63, p = 0.09). Median scores, however, differed substantially (0.69 versus 0.60), a difference exceeding the minimal important difference of both instruments. Agreement was low, with an intra-class correlation of 0.45.Finally, we found large differences in measuring change over time. The SF-6D recorded greater intra-subject change in the PTCA-group. Only the EQ-5D recorded significant change in the CABG-groups. In the latter groups changes in SF-6D domains cancelled each other out. CONCLUSION: Although both instruments appear to measure similar constructs, the EQ-5D and SF-6D are quite different. The low agreement and the differences in median values, scoring range and sensitivity to change after intervention show that the EQ-5D and SF-6D yield incomparable scores in patients with coronary heart disease.