Inclusion of metabolomic analysis in animal experiments offers unique perspective into how treatment responses are manifested as the final products of biological processes. Metabolomics offers a rapid, non-invasive approach to uncover specific metabolic fingerprints that are closely related to phenotype. The metabolome itself is a complex mixture of thousands of metabolites that are identified using high-throughput metabolomics platforms based on nuclear magnetic resonance (NMR) or mass spectrometry (MS). These platforms facilitate evaluation and integrated analysis of nutritional or therapeutic strategies, metabolic profiling of disease states and the identification of predictive biomarkers for the risk of disease. In dairy research, the use of metabolomics is becoming increasingly popular. The transition period in dairy production systems is associated with increased risk of metabolic diseases, particularly ketosis, metritis, mastitis, and retained placenta. Recent studies have sought to establish metabolic biomarkers, while metabolomic profiling reveals commonality among several diseases. Similarly, temporal profiling indicates metabolites associated with the development of ketosis change with disease progression, which may aid in identification of at-risk individuals. Identification of a health metabotype through the transition period has also been investigated as an innovative approach to extend the productive lifespan of the lactating dairy cow. Our own research has focused on the identifying the effects of nutritional programming on metabotype development in dairy heifers from neonates to mature, lactating cows. We found that an enhanced calf milk replacer feeding scheme in dairy heifers in early life appears to establish a lipid oxidative metabotype that is associated with elevated milk fat yield, maintenance of body condition and improved survival in first lactation. Lipid-associated metabolites are commonly identified in metabolomic evaluations in dairy cattle studies, indicating opportunity to develop nutritional and management strategies around these biomarkers. Used in conjunction with other measurements and technologies, metabolomics offers a fast and reliable tool for researchers to more fully elucidate metabolic adaptations toward understanding complex biological systems.