Complex diseases represent a number of common disorders such as allergic conditions, cardiovascular, metabolic and chronic inflammatory diseases. These diseases are caused by a combination of genetic, environmental and lifestyle factors. This complex etiology creates challenges when it comes to diagnostics, follow-up programs and treatment. Although exact disease mechanisms are yet to be elucidated for most complex diseases, key genetic determinants have been mapped and omics profiling has unraveled involved pathways. Using this wealth of data, precision medicine applications have started to appear also for common, complex diseases. In this article, we review current precision medicine applications from a clinical point of view and outline briefly a roadmap ahead for further clinical implementation of precision medicine in complex diseases.