Next-generation sequencing (NGS) has great potential to tailor the treatment of patients to their cancer genome alterations. Case reports, retrospective analysis of phase I trials, open studies of targeted therapies in population enriched in particular genotypes, and series of breast and lung cancer patients have shown encouraging clinical outcome for the matching of drugs to specifi c molecular alterations.Ongoing clinical trials are testing how NGS of tumors can guide individualization of treatment and whether the integration of the NGS into patient care can translate into superior patient outcome. The use of NGS comes with multiple challenges such as access to tumor material, data interpretation, and adaptation of regulatory frameworks for drugs targeting small population and for complex molecular diagnostics. Analytical validation of sequencing platforms and gene panels, access to multiple therapies addressing new targets and development of blood-based tests will support the expanding role of NGS in drug development and clinical trials.