Modern food analysis is directed to the characterization of as many components as possible in food and food-related materials. The use of -omics technologies within a Foodomics approach requires the use of high throughput analytical techniques able to offer increased resolving power and capability to separate a high number of compounds. From this perspective, two-dimensional liquid chromatography has the potential to unravel very complex food matrices, providing with high resolving power and enhanced identification potential, particularly when coupled to mass spectrometry. This review presents an overview including the most notable two-dimensional liquid chromatography applications developed in the last ten years to study food safety, food quality and the relationship between health and food as well as for the characterization of particular groups of food components within a Foodomics perspective. Moreover, the latest developments and advances, limitations, future evolution and needs related to the use of this technique are critically discussed and commented.