All eukaryotic organisms like plants, animals, fungi and protists represent chimera from the fusion of free-living independent organisms by a process called endosymbiosis. Due to a mutual advantage for both, the host and the symbiont, this intracellular cooperation perpetuated and became irreversible. The endosymbiotic process was accompanied by transfer of genes to the host nucleas as well as gene loss, thereby coordinating cell development and differenciation under one central, namely nuclear control. Gene transfer from the endosymbionts is not complete and may be still ongoing, therefore both mitochondria and plastids have retained their own genome, which seems essentiell under most circumstances in all eukaryotic organisms. Maintenance of organellar genomes as well as of the transcription and translation machinery is an extensive and costly task for the parent cell. Until today it is not entirely understood, though hypotheses exist, why gene transfer has not gone to completion. The fusion and mixing of genomes offered a once in a life time opportunity to redesign biosynthetic and metabolic duties in the arising now compartmentalized eukaryotic cell. Therefore proteins of different genetic origin can be found in almost every subcellular compartment. The division of labour principle made the eukaryotic cell very successful, which is surprising, since it lost biochemical diversity and flexibility in comparison to its bacterial anchestors. Evolution has produced a large variety of specialized organelles either in different tissues of one organism, like the plastid family in plants, or specialized in different organisms, even sometimes functionally very rudimentary but specially equipped organelles like hydrogenosomes, mitosomes or apicoplasts. They occur frequently in protists or parasites of medical relevance like Trichomonas vaginalis or Plasmodium falciparum. The Collaborative Research Centre Transregio 1 named "Endosymbiosis: From Prokaryotes to Eukaryotic Organelles" was funded by the Deutsche Forschungsgesellschaft for twelve years from 2000 - 2012. Scientists from the Universities of Düsseldorf, Marburg und Munich joined forces to understand the underlying molecular processes, which allowed endosymbiosis to occur and successfully establish mitochondria and chloroplasts, their biogenesis, differentiation, function and inheritance. This special volume comprises the work done and progress made in the research area of the different projects funded through the CRC - TR1 on Endosymbiosis. I would like to thank all the contributors for their impressive and timely contribution.