Breast-feeding is the ideal nutrition for a newborn’s integral necessities. It seems crucial therefore to know its composition in order to provide suitable infant formula when required. Of these, polyamines (with lactation and the microbiota being its intestinal source) are involved in the development of gut epithelium and immunity. Safety concerns limit human intervention studies. Therefore, we studied the amounts of polyamines supplied by breast milk (varying among mothers) or infant formula feeding, up to day 30 postpartum, in the faeces of newborns. Independent samples (68) of breast milk from fifty-nine healthy Caucasian woman (day 0, 1, 3, 5, 7, 15 and 30 postpartum) who had natural deliveries after week 38, same-day faeces of newborns when available (eighty-one from breast milk and fifty-five from infant formula fed) and six infant formulas were collected and the polyamine content was determined by HPLC. In breast milk, polyamines and isoamylamine (a primary amine), with inter-individual variations, increased over time (with a higher content of spermidine; no other amines were present). Overall, they were much higher than in infant formula. By the 2nd week after birth, polyamines, cadaverine and tyramine, but not isoamylamine, were higher in the faeces of those fed infant formula compared with those fed breast milk. Cadaverine and tyramine could be used to predict the feeding type used for newborns. The differences in the content may be related to distinct colonisation of amine-producing bacteria, which can be established by polyamines. Further studies are required to determine the clinical utility of these findings.