Coronary heart disease is a major health priority area in Australia. Cholesterol-lowering agents are generally considered to be cost effective for the secondary prevention of coronary heart disease. There is growing evidence, however, that the effectiveness of statins varies from one individual to another. The Taq1B polymorphism is an example of a genetic polymorphism that is thought to influence the effectiveness of statins. The aim of the current analysis is to estimate the cost-effectiveness of genetically screening coronary heart disease and stroke patients for the Taq1B polymorphism, and prescribing statin treatment to those with the B1B2 or B2B2 forms of the gene. A health sector perspective was adopted with a maximum acceptable cost-effectiveness ratio set at AUS$50,000/disability-adjusted life year. There is an 89% probability that screening and prescribing statins to those with the B1B2 and B2B2 alleles is more cost effective than prescribing statins to all patients. Modeling the cost-effectiveness of pharmacogenetics in major areas of medicine provides useful information to help in resource allocation and decision making. Economic evaluations similar to this one will be required in the future as the results of further clinical trials to establish the effectiveness of statins based on genotype become available.