The increasing performances of analytical techniques, especially two-dimensional liquid chromatography hyphenated with highly sensitive detectors, allow discovery of new targeted compounds in highly complex samples, whether biomarkers in environmental effluents, natural metabolomes in natural products or unknown impurities in synthetic chemical process. While structural identification can usually be achieved through mass spectrometry and databases, it can be useful to confirm the potential structure via NMR analysis and/or to obtain standard reference material for quantitative purposes, incentive for the production of μg to mg of new target compounds. Hence, preparative chromatography, which was initially run for large-scale production, is now facing new challenges, with small volumes of highly complex samples to deal with. Unfortunately, one dimensional chromatographic methods exhibit limited performances when targets are minor compounds in a complex matrix. Moreover, for process intensification or limited amount of sample, it is now a priority to be able to isolate multiple components with the largest yield possible using as few purification steps as possible. With these specifications in mind, a comprehensive multidimensional chromatographic method for preparative purposes is becoming appealing.