Phenotyping requires measuring traits chosen for their socio-economic importance or their cognitive value. Needs for phenotyping depend on the trend in breeding methods and production systems, and also on technological developments allowing for high throughput standardised approaches at a reasonable cost. Considering animal breeding, implementation of genomic selection introduces the concept of reference population, where specific phenotypes not routinely available can be obtained to associate genetic markers with performance. Association between markers and phenotypes also open the way towards individual diagnostic to support herd management. Robotics and individual electronic identification require important investments but offer quite new prospects for phenotyping traits such as feed efficiency or behaviour. Complementary tools are provided by technological developments in functional genomics and by spectral analysis of proteins, which can unravel underlying mechanisms and refine the definition of phenotypes at the molecular scale. The concept of biomarker has emerged in human medicine in order to predict phenotype and is expected to be applied also to farm animals. The closer the phenotyping is from the biological mode of action, the more accurate will be the detection of genes determining phenotypic variation. More particularly, the search for genome regions controlling gene expression (eQTL) makes possible to explore the mechanisms responsible for the variability of complex traits. Great progress can thus be expected for the identification of genes underlying QTL thanks to simultaneous improvements in phenotyping and genome sequencing..