Lipidomics and integrative multi-omics methods are emerging rapidly. In this chapter, we highlight the role that lipidomics data can play in multi-omics studies. We exemplify how lipidomics data have contributed to insights in recent multi-omics studies. We describe specific considerations on the experimental methods and give an overview of relevant integrative computational analysis approaches. The experimental design must be adapted to the multi-omics context, and data analysis challenges must be considered. Finally, we summarize the great potential of lipidomics data in multi-omics and suggest ways in which the knowledge from such multimodal analysis sets can be further increased.