Chloroplast biogenesis involves a specific bacterial type plastid-encoded RNA polymerase (PEP). Biochemical experiments revealed that the core bacterial multisubunit enzyme PEP was surrounded by 12 PAPs (PEP-associated proteins) that are essential for chloroplast biogenesis. A deeper understanding of the roles of each protein would improve the understanding of chloroplast biogenesis. In this paper we explain the different techniques used to isolate selected PAPs : PAP 1, 2, 3 and 11. This knowledge will be essential in deciphering fundamental biochemical pathways which will help in the development of more efficient and productive plants for new generation agricultures.