The chloroplast is the site of photosynthesis and many other essential plant metabolic processes, and chloroplast development is an integral part of plant growth and development. Mutants defective in chloroplast development can display various color phenotypes including the intriguing virescence phenotype, which shows yellow/white coloration at the leaf base and greening toward the leaf tip. Through large scale genetic screens, we identified a series of new virescent mutants including virescent3-1 (vir3-1), vir4-1, and vir5-1 in Arabidopsis thaliana. We showed that VIR3 encodes a putative chloroplast metalloprotease by map-based cloning. Through site-directed mutagenesis, we showed that the conserved histidine 235 residue in the zinc binding motif HEAGH of VIR3 is indispensable for VIR3 accumulation in the chloroplast. The chloroplast localization of VIR3 was confirmed by the transient expression of VIR3-GFP in leaf protoplasts. Furthermore, taking advantage of transgenic lines expressing VIR3-FLAG, we demonstrated that VIR3 is an intrinsic thylakoid membrane protein that mainly resides in the stromal lamellae. Moreover, topology analysis using transgenic lines expressing a dual epitope-tagged VIR3 indicated that both the N and C termini of VIR3 are located in the stroma, and the catalytic domain of VIR3 is probably facing the stroma. Blue native gel analysis indicated that VIR3 is likely present as a monomer or part of a small complex in the thylakoid membrane. This work not only implicates VIR3 as a new factor involved in early chloroplast development but also provides more insight into the roles of chloroplast proteases in chloroplast biogenesis.Chloroplasts not only serve as the site of photosynthesis but also are responsible for the production of many essential metabolites in higher plants. Although a descendant of photosynthetic prokaryotic organisms through endosymbiosis, the chloroplast has evolved many unique features including complex regulatory networks to achieve the coordinated expressions of plastid genome and nuclear genome and the coordination of chloroplast development with leaf development (1, 2). Given the importance of the chloroplast, much research has been directed at dissecting the intricate pathways that regulate chloroplast development. One fruitful way has been the identification of mutants that are defective in nuclear genes for chloroplast proteins. Large scale genetic screens have revealed that mutants of nuclear genes for chloroplast proteins can give rise to myriads of visible leaf color phenotypes ranging from albino, yellow, and pale green to virescence and variegation (3).Among the many types of mutants that are associated with chloroplast defects are the intriguing virescent mutants. These mutants display young and emerging tissues that are deficient of photosynthetic pigments, a sign that is often associated with underdeveloped plastids (2, 4). As leaves expand, however, these tissues gradually become greener along the leaf proximaldistal axis. At the whole plant level, the ce...