Autophagy plays important roles in physiologic cellular events and also in cancers. It has been reported that cells escaped from death via autophagy and if autophagy inhibited, cells conducted to apoptosis. In some studies, protective effects of the melatonin on induced autophagy in cancer cells reported. In this study, we aimed to evaluate the autophagic effect of melatonin in cancer stem cells. For this purpose, CD44+/CD24- phenotype cells sorted from melatonin-treated and untreated MCF-7 and HEK293 cells. Effect of melatonin on autophagy was analysed by immunofluorescence and western blot analysis. Results showed that melatonin-induced LC3 (Microtubule-associated protein 1A/1B-light chain 3) aggregation and formation of autophagic vacuoles in MCF-7 derived cancer stem cells and also induced LC3-I to LC3-II conversion in these stem cells when compared to untreated control group. In conclusion, melatonin showed a pro-autophagic effect in CD44+/CD24- stem cells derived from MCF-7 cells and anti-autophagic effect in CD44+/CD24- stem cells obtained from HEK293 cells.