Modern molecular nutrition focuses on health promotion, disease prevention and performance improvement through diet. In analogy to Pharmacogenetics and -genomics, the disciplines “Nutrigenetics” and “Nutrigenomics” have evolved. Nutrigenetics asks how individual genetic disposition, manifesting as single-nucleotide- and copy-number polymorphisms as well as epigenetic regulation, affects susceptibility to diet. Nutrigenomics addresses the inverse relationship, i.e. how diet influences gene transcription, protein expression and metabolism. The long-term objective of Nutrigenomics is personalised nutrition for maintenance and improvement of individual health and for disease prevention. Transcriptomics can put Proteomics- and Metabonomics-derived markers into a larger biological perspective. Metabonomics is a diagnostic tool for metabolic classification of individuals with the asset of quantitative, non-invasive analysis of easily accessible human body fluids such as urine, blood and saliva. This feature also applies to some extent to Proteomics, with the constraint that the latter discipline is more complex in terms of composition and dynamic range of the sample. Apart from addressing the most complex “Ome”, Proteomics represents the only platform that delivers not only markers for disposition and efficacy but also targets of intervention. Application of integrated Omic technologies will drive the understanding of interrelated pathways in healthy and pathological conditions and will help to define molecular ‘switchboards’, necessary to develop disease related biomarkers. This will contribute to the development of new preventive and therapeutic strategies for both pharmacological and nutritional interventions. This paper reviews inflammatory gut disorders, the state-of-the-art of the three Omics platforms and discusses the implication of the latter in biomarker revelation for nutritionally actionable inflammatory disorders in the intestine.