Introduction:Our aim was to investigate biomarkers of neonatal pain and their association with two pain scales.Methods:This prospective study included 54 full-term neonates. Levels of substance P (SubP), neurokinin A (NKA), neuropeptide Y (NPY), and cortisol were recorded and two pain scales (Premature Infant Pain Profile [PIPP] and Neonatal Infant Pain Scale [NIPS]) were used.Results:A statistically significant decrease in the levels of NPY (p= 0.02) and NKA (p= 0.03) was detected. A significant increase in NIPS scale (p< 0.001) and PIPP scale (p< 0.001) postpainful intervention was also detected. There was a positive correlation between cortisol and SubP (p= 0.01), NKA and NPY (p< 0.001) and between NIPS and PIPP (p< 0.001). A negative correlation was found for NPY with SubP (p= 0.004), cortisol (p= 0.02), NIPS (p= 0.001) and PIPP (p= 0.002).Conclusions:Novel biomarkers and pain scales may help in designing an objective tool for the quantification of neonatal pain in the everyday practice.