For most traits in nature, the phenotype is quantitative, i.e., can be quantified and its continuous frequency in a population follows a normal distribution. Such traits are termed as complex or quantitative traits, and are defined as phenotypes that vary in degree and can be attributed to polygenic effects, i.e., product of two or more genes and their environment. These include economically important traits of crops and animals, and human diseases viz. cancers, diabetes, neurological disorders and ageing. The identification of genetic loci that modulate and regulate these traits, termed as quantitative trait loci (QTL), is difficult due to locus heterogeneity, gene-gene interactions, low penetrance, variable expressivity and pleiotropy. Additionally, environment is a major confounding factor in modulating these traits. Thus, determining the genetic factors that condition these phenotypes has been one of the main challenges for genetics. However, recent, technological advances, such as high-throughput phenotyping and genotyping of large segregating and natural populations, are making it possible to dissect the genetic factors contributing to these traits and we have begun to understand their molecular basis.