Recessive mutations are known to give rise to cell lineage-type leaf variegation that forms green and white sectors due to arrested chloroplast development. The yellow variegated 2 (var2) mutant in Arabidopsis thaliana has been studied as a typical leaf-variegated mutant whose defect results from the lack of FtsH2 metalloprotease in chloroplasts. To understand physiological properties of variegated sectors, gene expression profiles were investigated between green and white sectors of var2 leaves. Consistent with impaired thylakoid formation, a substantial number of genes related to photosynthesis and chloroplast functions were repressed in white sectors. In addition, many genes were up-regulated in white sectors. Since var2 leaves suffer from photooxidative stress and accumulate high levels of reactive oxygen species (ROS) due to compromised Photosystem II repair, we focused ROS scavenging genes such as Cu/Zn superoxide dismutase 2 (CSD2). Activation of CSD2 was specific to white sectors and appeared to be under the control of copper availability. A lack of thylakoid membranes in white sectors perhaps leads to excess free copper and iron conditions, thus white sectors mimic a copper sufficient condition. We infer that CSD2 acts not only on ROS detoxification but also on copper buffering. Interestingly, an up-regulation of Cu/Zn SOD was commonly observed in various variegated leaves. Our findings thus highlight the crucial role for the control of oxidative stress and free metals in variegated leaf sectors.