The BCL2 family has both pro-apoptotic and anti-apoptotic functions. Furthermore, stem cell markers such as Oct4, SOX2, and NANOG enhance cancer cells’ self-renewal, resistance to anti-cancer drugs and clonal growth. Therefore, selective inhibition of BCL2 genes and downregulated expression of stem cell markers should reduce the survival of cancer cells. Previous studies have reported that lutein, a carotenoid pigment present in fruits and vegetables, can inhibit cancer cells. However, the inhibitory effects of lutein on cancer cells have not been investigated sufficiently. In this study, we used gene expression analysis by polymerase chain reaction (PCR) and Western blotting to show that lutein regulates the expression of genes involved in apoptosis and several stem cell marker genes in a human lung cancer cell line, A549. Lutein induced gene expression of pro-apoptotic BAX and CAS3 and reduced the level of the anti-apoptotic gene BCL2. Furthermore, protein expression of BCL2 and BAX was regulated by treatment with lutein. Lutein also inhibited SOX2 and NANOG gene expression in A549, but not POU5F1. In addition, lutein reduced gene expression of SLCA11, but induced CD44 and CD133 gene expression. These results indicated that lutein inhibits several events associated with apoptosis regulation in a BCL2 family-dependent pathway.