Metabolomics, the study of the whole profile of small molecules in an organism, is shaping up to be one of the omics technologies with the highest potential to bridge the gap between the genome and phenome. In livestock breeding, the ability to associate genetic background with intermediate phenotypes (i.e. metabolites) that influence production traits is extremely valuable. However, metabolomics is still in its infancy, especially in the context of animal breeding. An overview of the state of the art of metabolomics research in cattle is given, including a brief introduction, and a summary of approaches for data collection and analysis. Also considered is the relationship between metabolomics and production traits as well as genetic background, along with the integration of genomics, metabolomics and phenomics in animal breeding programs.