The applications of omics (genomics, transcriptomics, proteomics and metabolomics) technologies in nutritional studies have opened new possibilities to understand the effects and the action of different diets both in healthy and diseased states and help to define personalized diets and to develop new drugs that revert or prevent the negative dietary effects. Several single nucleotide polymorphisms have already been investigated for potential gene-diet interactions in the response to different lipid diets. It is also well-known that besides the known cellular effects of lipid nutrition, dietary lipids influence gene expression in a tissue, concentration and age-dependent manner. Protein expression and post-translational changes due to different diets have been reported as well. To understand the molecular basis of the effects and roles of dietary lipids high-throughput functional genomic methods such as DNA- or protein microarrays, high-throughput NMR and mass spectrometry are needed to assess the changes in a global way at the genome, at the transcriptome, at the proteome and at the metabolome level. The present review will focus on different high-throughput technologies from the aspects of assessing the effects of dietary fatty acids including cholesterol and polyunsaturated fatty acids. Several genes were identified that exhibited altered expression in response to fish-oil treatment of human lung cancer cells, including protein kinase C, natriuretic peptide receptor-A, PKNbeta, interleukin-1 receptor associated kinase- 1 (IRAK-1) and diacylglycerol kinase genes by using high-throughput quantitative real-time PCR. Other results will also be mentioned obtained from cholesterol and polyunsaturated fatty acid fed animals by using DNA- and protein microarrays.