Abstract Introduction Women who have problems with lactation can use human milk banks. Mainly this human milk is provided to premature babies and sick newborns. Human milk is the most suitable food for newborns and infants, recommended by WHO (World Health Organization). Human milk has anti-inflammatory, anti-infective, and anti-allergic properties, and also works for immunomodulation. Melatonin has a special, underestimated importance in the composition of breast milk. It is a hormone that has many body functions and, for several decades, its antioxidant potential has been increasingly talked about. The aim of the study was to examine the effect of Holder pasteurization on melatonin concentration in human milk. Materials and Methods 18 samples of human milk from donors from the human milk bank were used for the analysis. Melatonin concentration before and after pasteurization was determined by ELISA. In addition, the nutritional content composition of milk was analyzed using MIRIS Human Milk Analyzer and correlations examined. Results Melatonin concentration in human milk before pasteurization was 0.65–26.24 pg/mL (Me=9.58, IQR=12.72), while after pasteurization 0.80–29.58 pg/mL (Me=9.98, IQR=11.26). There was a positive correlation between melatonin concentration before and after pasteurization (r=0.797, p<0.001). Conclusions The Holder pasteurization process does not affect the concentration of melatonin in milk samples, which may be a recommendation for human milk banks.