While it has been established that binary fission of leaf chloroplasts requires the prokaryote-derived, division site determinant protein MinE, it remains to be clarified whether chloroplast division in non-leaf tissues and the division of non-colored plastids also involve the MinE protein. In an attempt to address this issue, plastids of cotyledons, floral organs, and roots were examined in the Arabidopsis thaliana mutant of the MinE (AtMinE1) gene, which was modified to express the plastid-targeted cyan fluorescent protein constitutively, and were quantitatively compared with those in the wild type. In the cotyledons, floral organs, and root columella, the plastid size in the atminE1 mutant was significantly larger than in the wild type, while the plastid number per cell in atminE1 appeared to be inversely smaller than that in the wild type. In addition, formation of the stroma-containing plastid protrusions (stromules) in the cotyledon epidermis, petal tip, and root cells was more active in atminE1 than in the wild type.