Nutrition sciences apply transcriptomics, proteomics and metabolomics to molecularly assess nutritional adaptations. Transcriptomics can generate a holistic overview on molecular changes to dietary interventions. Proteomics is most challenging because of the higher complexity of proteomes as compared to transcriptomes and metabolomes. However, it delivers not only markers but also targets of intervention, such as enzymes or transporters, and it is the platform of choice for discovering bioactive food proteins and peptides. Metabolomics is a tool for metabolic characterization of individuals and can deliver metabolic endpoints possibly related to health or disease. Omics in nutrition should be deployed in an integrated fashion to elucidate biomarkers for defining an individual's susceptibility to diet in nutritional interventions and for assessing food ingredient efficacy.