Background: Stem cell technology is a promising research area with a potential to create effective therapies for many degenerative diseases. However, to apply stem cell technology, we need to be able to identify and understand mechanisms that distinguish healthy regeneration processes from processes, which may result in chronic inflammation, scarring, fibrosis or cancer. GHK-Cu (glycine-L-histidine-lysine) is a small copper-binding peptide, which has a remarkable and well-documented ability to improve wound healing and tissue regeneration, regulate remodeling of connective tissue and synthesis of collagen, elastin and glycosaminoglycans, reduce inflammation and scarring, increase antioxidant-enzymes and protect cells from toxic by-products of lipid peroxidation. Methods: Authors used a computer-based gene profiling tool, The Connectivity Map, to identify a number of human genes regulated by GHK, relevant to regulation of cell differentiation, apoptosis and stem cell function. Results: The number of human genes associated with stem cell function was 57 genes in the range of increases of 50% UP and 46 genes in the range of decreases of 50% DOWN. Conclusion: Based on laboratory data and gene profiling data, GHK-Cu may be used to improve stem cell therapy and to help shift regeneration processes to healthy regeneration.