Aloe-emodin (1, 8-dihydroxy-3-hydroxyl-methylanthraquinone; AE) and emodin (1,3,8-trihydroxy-6-methylanthraquinone; EM) are anthraquinone derivatives that have been detected in some medical plants andshare similar anthraquinone structures. AE and EM have been shown to exhibit anticancer activities in variouscancer cell lines; however, the inhibitory effects of these derivatives on the growth of cancer cells were previouslyreported to be different. Gastric cancer is the second most common cause of cancer cell death worldwide. In thepresent study, we examined the inhibitory effects of 0.05 mM AE and 0.05 mM EM on the proliferation of theMKN45 human gastric cancer cell line. The proliferation of MKN45 cells was significantly inhibited in AE- andEM-treated groups 24 h and 48 h after treatment. Furthermore, the inhibitory effects of EM were stronger thanthose of AE. The cell cycle of MKN45 cells were arrested in G0/G1 phase or G0/G1 and G2/M phases by AE andEM, respectively. However, an analysis of intracellular polyamine levels and DNA fragmentation revealed thatthe mechanisms underlying cell death following cell arrest induced by AE and EM differed.