The exponential advances in cutting-edge technologies and informatics tools utilized in biomedical science to generate and process high-throughput biological data sets (omics data) have permeated into the realm of animal science, and more specifically dairy cattle nutrition and physiology. Omic tools including genomics, epigenomics, transcriptomics, proteomics, and metabolomics produce large amounts of data that need appropriate bioinformatic analyses to derive meaningful conclusions. Omic technologies will help in the discovery of biological markers due to various physiological, management, and environmental factors such as lactation, nutrition, and heat stress. The merging of omics and bioinformatics represent the foundation of systems biology, a field of study broadly use in modeling organisms to enhance the understanding of the complex biological interactions occurring within cells and tissues at the gene, protein, and metabolite level. These complex interactions can be orchestrated by major factors such as nutrition and physiology during critical life stages including late pregnancy, in utero development, or postnatal growth. Therefore, this review will give examples of the applications and benefits of the use of different omic tools in aspects related to the health and performance of dairy animals. For instance, transcriptomics in small ruminants revealed the negative impact of undernutrition on genes regulating milk synthesis and mammary cell proliferation while activating apoptosis and involution. Changes in the bovine mammary gland transcriptome during the transition from late pregnancy to lactation has revealed the contrasting upregulation of genes associated with milk synthesis while downregulating those related to cell proliferation. Studies on miRNAs from goat and sheep mammary gland have shed light on the potential regulatory mechanisms these non-coding RNAs have during the onset of lactation. Omics research is limited in ruminants, especially in small ruminants. However, the increasing adoption of these technologies will provide new avenues for integrative research across and within tissues with the goal to develop new nutritional management approaches to achieve better animal health and production.