OBJECTIVES: Previous studies suggest prasugrel may be cost effective when compared to clopidogrel for treating acute coronary syndrome patients (ACS).  Recent research has shown that the reduced function allele CYP2C19*2 (*2 allele) is associated with an increased risk of adverse events for ACS patients taking clopidogrel and a decreased risk for patients taking prasugrel.  The purpose of this paper is to test whether using clopidogrel for all patients is cost effective compared to  prasugrel for *2 allele patients in combination with clopidogrel for non *2 patients and to prasugrel only for New Zealand. METHODS: Effectiveness of clopidogrel and prasugrel from published TRITON-TIMI 38 clinical trials was combined with rates of *2 occurrence in Maori, Pacific Islanders, Asian and NZ European and national hospital records on rates and costs of hospitalisations 15 months post ACS for stroke, MI, bleeding, stent thrombosis and cardiovascular  death.  Decision tree modelling and Monte Carlo simulations examined the robustness of the results.   RESULTS: Rates of the *2 allele differ significantly between NZ European (15%), Maori (24%), Asian (29%) and Pacific People (45%).  Analysis of hospital records suggest that rates of MI, stroke, bleeding, stent thrombosis and cardiovascular death were much higher in the general New Zealand population than in the clinical trial population.  The cost effectiveness analysis suggests that use of a genetic test to guide combined use of clopidogrel and prasugrel was cost effective for most age and ethnic groups, but particularly for Maori males (NZ$3184/QALY), Maori females (NZ$3687/QALY), Pacific men (NZ$4617/QALY) and Pacific women (NZ$7605/QALY).  Prasugrel is more costly and less effective than clopidogrel. CONCLUSIONS: The results here suggest that the use of a genetic test to guide treatment decisions for ACS patients is cost effective, especially for Maori and Pacific peoples, and that prasugrel alone is not cost effective in New Zealand.