Colorectal cancer (CRC) is the most common cancer in Singapore. We sought to evaluate the long-term cost-effectiveness of targeted genetic testing and surveillance programs in individuals at high risk of hereditary non-polyposis colorectal cancer (HNPCC), as compared to an unselective clinical surveillance program alone in Singapore. A Markov model analysis from the healthcare service provider's perspective was developed to follow over a lifetime a cohort of cancer-free 21-year-old individuals, who were first-degree relatives of HNPCC patients with a known mutation. Genetic testing strategy provided a lifetime saving of Singapore dollars (SGD) 13,588 per person and gained additional life years of 0.01, as compared to clinical surveillance alone, by sparing non-mutation carriers from unnecessary and invasive intensive clinical surveillance (assuming 100% compliance with recommended surveillance programs in both strategies). Sensitivity analyses showed that as long as the compliance rate in mutation carriers was not lower than that for individuals without genetic testing, pursuing a genetic testing strategy would either be a more favorable option with discounted incremental cost-effectiveness ratios ranging from SGD 6,961 to 17,289 per life year gained or a dominant status achieved (more life year gained and less costly). Genetic testing for individuals at high risk of HNPCC allows targeted clinical surveillance to be directed at mutation carriers, ensuring efficient use of healthcare resources and reduces CRC-related mortality. It can be regarded as a cost-effective strategy in Singapore, if an improved compliance with recommended surveillance protocol is achieved in proven mutation carriers.