Chloroplasts are plant cell-specific organelles that perform photosynthesis and biosynthesis of many important metabolites. They are the energetic and biochemical base for the terrestrial biosphere of our planet. Despite their importance we know almost nothing about how these complex organelles are generated. We aim to identify the primary processes and molecular key regulators that control the biogenesis of chloroplasts. To this end we use newly identified Arabidopsis mutants that are defective in the expression of polymerase-associated proteins (PAPs). The group of PAPs is comprised of twelve nuclear encoded proteins of wide functional variety that surround the bacteria-like core complex of the plastid encoded RNA polymerase (PEP). Formation of the PEP complex appears to be a bottleneck in the biogenesis of chloroplasts. If one of the PAPs is missing the whole PEP complex is either not formed or becomes unstable. As a result plastid transcription by the PEP complex becomes arrested and chloroplast biogenesis in these mutants is blocked leading to an albino phenotype. Electron micrographs demonstrate that this block occurs at the very first step of thylakoid membrane formation directly after vesicle formation at the inner envelope membrane. The albino plastids do not generate a thylakoid membrane system due to a combination of four molecular defects that are all caused by the PEP deficiency. The combination of these defects, thus, prevents that the undeveloped plastid proceeds towards the chloroplasts stage. This arrested development allows a detailed analysis of the developmental step just before chloroplast generation. Gene expression profiling indicates that light-grown albino pap mutants express light-regulated genes like light-grown green wildtype but exhibit gene expression characteristics of dark-grown plants for metabolism genes. In these mutants the processes of photomorphogenesis and chloroplast biogenesis can be genetically uncoupled.