Eukaryotic cells have a complex organization into membrane-delimited organelles. Whereas we have been steadily accumulating mechanistic data on the organization and regulation of these compartments, far less is understood about their origins and evolution. I will discuss our recent work in the evolutionary analysis of three types of intracellular compartments: endosymbiotic, endomembranous, and microtube-derived. To study evolution at a this level we are having to develop new sets of tools, from neutral models at the whole genome evolution level, sequence classification methods, ways to link molecular information with morphology and databases. I will discuss how we are using these tools to discover new principles and new molecular components. Unexpectedly, this evolutionary approach is leading us to new ways of finding drugable targets and to reposition existing drugs.