Large amounts of lipidomics data are rapidly becoming available. However, there is a lack of tools capable of taking the full advantage of the wealth of new information. Lipid bioinformatics is thus an emerging need as well as challenge for lipid research. Lipid concentration changes in biological systems reflect regulation at multiple spatial and dynamic scales, e.g., biochemical reactions in the cells, intercellular lipid trafficking, changes in cell membrane composition, systemic lipid metabolism or lipid oxidation. In order to address the complexity of lipids and their regulation, four areas of bioinformatics need to be developed: (1) data processing and lipid identification, (2) statistical data analysis, (3) pathway analysis, and (4) lipid modeling in systems and biophysical contexts. In this paper we overview the current state of the lipid bioinformatics field as well as suggest few potential new areas of research.