BACKGROUND: Generic health preference measures that capture quality of life improvements in depression are important for economic analysis of new technologies. AIM: To compare two widely used preference measures, the EQ-5D and SF-6D, in terms of their dimensions and health utility values. METHOD: EQ-5D and SF-6D data collected from 114 patients with depression, who participated in a cluster, randomised controlled trial to evaluate a collaborative care intervention in UK, primary care practices. Utilities were examined across the whole sample and by level of depression severity using the PHQ-9. RESULTS: Depression was associated with disutility at baseline. At 3 month follow-up mean utility increased 0.147 for EQ-5D and 0.082 for SF-6D. Health gains were observed in patients in remission from depression and those with the mildest level of depression severity. CONCLUSIONS: Both generic preference measures were sensitive to health gains in depression within a relatively short follow-up period; larger health gain was observed for the EQ-5D.