Recently, Companion Diagnostics (CoDx) have been gaining importance to promote personalized medicine in order to improve the safety and cost effectiveness of therapy. In July 2011, the FDA published draft guidance for the development of CoDx, which recommends the co-development of CoDx and new drugs as the best practice, and then the FDA approved vemurafenib and the BRAF-V600-E gene mutation assay simultaneously as a typical example of the co-development of a new drug and its CoDx. Considering medical needs for multiple biomarker assays to select the right assay from various therapeutic candidates, more complicated assay technologies such as DNA sequencing will be required for CoDx in the near future. However, since it is quite difficult to standardize the validation process and manage test quality under the current regulatory criteria of in-vitro diagnostics using advanced and/or complicated assay technologies, the clinical use of laboratory-developed tests (LDT) should be recommended in order to avoid biomarker test lag. On the other hand, the current reimbursement system is not always suitable to assess the clinical and technological value of CoDx and it should be revised to encourage the development of CoDx. Although Health Technology Assessment (HTA) is a potential method to assess the value of CoDx, it is not easy to define appropriate indicators for CoDx because its clinical utility and cost effectiveness are completely dependent on the performance and value of available therapy. It is also suggested that the price and/or insurance rate of CoDx should be included in the price of the drug; however, there is no good solution to how to pay for CoDx with negative results for all therapies. It is said that the concept of personalized medicine with advanced technologies is a destructive innovation that could markedly change the current structure and system of medications; therefore, it is essential to create a quite new regulatory and reimbursement system to provide patients with the right medicine at the right time.