OBJECTIVE : This study aimed to evaluate the performance of EQ-5D data mapped from SF-12 in terms of estimating cost effectiveness in cost-utility analysis (CUA). The comparability of SF-6D (derived from SF-12) was also assessed. METHODS : Incremental quality-adjusted life years (QALYs) and incremental cost-effectiveness ratios (ICERs) were calculated based on two Markov models assessing the cost effectiveness of haemodialysis (HD) and peritoneal dialysis (PD) using utility values based on EQ-5D-5L, EQ-5D using three direct-mapping algorithms and two response-mapping algorithms (mEQ-5D), and SF-6D. Bootstrap method was used to estimate the 95% confidence interval (percentile method) of incremental QALYs and ICERs with 1000 replications for the utilities. RESULTS : In both models, compared to the observed EQ-5D values, mEQ-5D values expressed much lower incremental QALYs (range - 14.9 to - 33.2%) and much higher ICERs (range 17.5 to 49.7%). SF-6D also estimated lower incremental QALYs (- 29.0 and - 14.9%) and higher ICERs (40.9 and 17.5%) than did the observed EQ-5D. The 95% confidence interval of incremental QALYs and ICERs confirmed the lower incremental QALYs and higher ICERs estimated using mEQ-5D and SF-6D. CONCLUSIONS : Compared to observed EQ-5D, EQ-5D mapped from SF-12 and SF-6D would under-estimate the QALYs gained in cost-utility analysis and thus lead to higher ICERs. It would be more sensible to conduct CUA studies using directly collected EQ-5D data and to designate one single preference-based measure as reference case in a jurisdiction to achieve consistency in healthcare decision-making.