Autophagy is a process in which cell membrane rearrangement allows for the sequestration and degradation of part of the cytoplasm. Many protein components of the autophagic mechanism and their corresponding genes have been identified in yeast cells by molecular genetics, and this has enabled researchers to identify homologues of these genes in mammalian and plant systems. Autophagy is involved in the starvation response in which part of the cytoplasm is degraded in order to produce essential substrates to allow the cell to survive during extreme substrate-limiting conditions. However, autophagy may also be important as a quality control mechanism in normal cells. By screening Arabidopsis thaliana T-DNA insert mutants, we isolated an A. thaliana mutant that lacks the AtTIC40 gene and found that the cotyledon cells of this mutant contained undeveloped plastids. Moreover, many toluidine-stained particulate structures were found in the vacuoles of these mutant cells. The images from electron microscopy suggested that some of these particulate structures were partially degraded chloroplasts. Furthermore, oil bodies were found in the cotyledon cells of mutant and wild-type plants, which suggests that the mutant seedlings were not “starved” under the experimental conditions. These results may indicate that under nutrient-sufficient conditions, plant cells remove abnormal plastids by autophagy and that this mechanism is involved in the quality control of organelles.