A functional polymorphism in the 5′flanking region of the serotonin transporter gene (17q11.2, 5-HTTLPR) alters the transcription of the 5-HT transporter gene and seems to be associated with depression and anxiety-related personality traits in humans. This effect appears to be the most pronounced in individuals who are homozygous for the low-expressing “S” allele who have experienced significant critical life events in the past. Animal studies now link this polymorphism to an increased stress reactivity of the hypothalamus–pituitary–adrenal (HPA) axis. In humans, it remains unknown whether this polymorphism by itself affects HPA axis or only in interaction with environmental factors. The aim of the present study was to investigate the role of the 5-HTTLPR polymorphism for the HPA axis in humans early in the development at a time when individuals were exposed to very few or no early adverse experiences so far.We genotyped DNA for the 5-HTTLPR polymorphism including the A/G single-nucleotide polymorphism (SNP) in 126 three-day old newborns. The newborn's stress response was stimulated by a heel prick which is a part of a routine medical procedure. The heel prick induced a significant biological (i.e., cortisol) stress response in all newborns. Newborns with the “S/S” genotype showed a significantly higher endocrine response in comparison to newborns with “L/L” or “S/L” genotype.In this sample of newborn babies, the 5-HTTLPR genotype affected the HPA stress response to painful stimulation irrespective of additional influence of pre- or perinatal environmental factors we measured.