Many important drugs such as penicillin were discovered by serendipity. Other major drugs like the cholesterol-reducing statins were discovered using more advanced technologies, such as screening of large chemical libraries. In all these cases, the mechanism of action of the drug were largely unknown at the time of their discovery and was unraveled later. With the realization that patients with apparently similar diseases – breast or prostate cancer, for example - respond differently to similar treatments, we have begun to understand that the molecular bases of what we thought is the same disease entity, are different. Thus, breast or prostate cancers appear to be sub-divided to smaller distinct classes according to their molecular characteristics. As a result, we are exiting the era where the treatment of many diseases is “one size fits all”, and enter a new era of “personalized medicine” where the treatment is tailored according to the patient’s molecular/mutational profile. Here, the understanding of the mechanism will drive the development of new drugs. This era will be characterized initially by the development of technologies to sequence individual genomes, transcriptomes, proteomes and metabolomes, followed by identification and characterization of new disease-specific molecular markers and drug targets, and by design of novel, mechanism-based drugs to these targets. This era will be also accompanied by complex bioethical problems, where genetic information of large populations will become available, and protection of privacy will become an important issue.