In past five years, genome-wide association study (GWAS) has proven to be a powerful and efficient study design in identifying genetic variants associated with complex diseases and traits. Many studies have been performed to explore the genetic basis of various complex diseases and traits. Genetic breakthroughs have been achieved in complex diseases and traits, such as oncology, diabetes, cardiology, psychiatric disorders, autoimmune and immune related diseases, height, weight, blood lipid, and pigmentation. Up to September 11th 2010, nearly 200 complex diseases and traits have been investigated by this approach, and more than 3000 diseases and/or traits related variants have been identified. In this review, we present an overview of GWAS in complex diseases and traits.