Plastids of higher plants are semi-autonomous cellular organelles that have their own genome and transcription-translation machinery. Examples of plastid functions are photosynthesis and biosynthesis of starch, amino acids, lipids and pigments. Plastid functions are encoded in approximately 120 plastid genes and approximately 3,000 nuclear genes. Although many embryo and seedling lethal nuclear genes are required for chloroplast biogenesis, until now deletion of plastid genes either had no phenotypic consequence (8 genes), or caused a mutant phenotype but did not affect viability (13 genes). Here we identify an essential plastid gene. By using the CRE-lox site-specific recombination system we have deleted clpP1 (caseinolytic protease P1), one of the three genes (clpP1, ycf1 and ycf2) whose disruption had previously only been possible in a fraction of the 1,000-10,000 plastid genome copies in a cell. Loss of the clpP1 gene product, the ClpP1 protease subunit, results in ablation of the shoot system of tobacco plants, suggesting that ClpP1-mediated protein degradation is essential for shoot development.