The aim of this review article is to summarize and compare the effects of melatonin and caffeic acid phenethyl ester (CAPE) on the relationship between mitochondrial functioning and apoptosis. References in this article were selected with an approach based on a comprehensive literature review by using MEDLINE/PubMed and Google Scholar databases which were scanned in the last six months without any restrictions. For each database, the review terms used are 'melatonin', 'caffeic acid phenethyl ester, both together and associated with other key words such as apoptosis and mitochondria. Evidential mitochondrial molecular backgrounds for diseases make these two molecule competitors, since both of them use the same pathways to cope with fundamentals of the diseases such as nuclear factor κ-light-chain-enhancer of activated B (NF-κB inhibition, induction of mitochondrial apoptosis in cancer cells, free radical scavenging effects, and antioxidant activities. The data reviewed in this paper provide a useful background for the understanding of some molecular details of melatonin and CAPE on several medical situation and diseases. Mutual usage of these two tremendous molecules might have a capacity to open new therapeutic approaches in near future.