During the last fetal stage of development and in the neonatal period, the hypothalamic-pituitary-adrenal (HPA) axis secretes cortisol (C), responsible for several physiologic processes. The claws were recently proved to be a useful, non-invasive matrix for long time-frame retrospective C levels analysis also in puppies (Veronesi et al. 2015, Theriogenology 84:791–796). Because of the scarce knowledge on canine perinatology, this study was aimed to assess the C concentrations in claws of newborn puppies collected at birth, 30 and 60 days of age, and to evaluate the possible influence of age, gender and type of birth on C claws accumulation. The study was performed on 58 large purebred, normal, healthy puppies, born by spontaneous or cesarean parturition. The mean C claws concentrations significantly decrease from birth (26 ± 16.39 pg/mg) to 30 (10 ± 4.53 pg/mg) and 60 (6 ± 3.12 pg/mg) days of age (p < 0.0001); a decrease was also seen from 30 to 60 days of age (p < 0.05). No influence of newborn gender and type of birth was found. This trend of decrease is in agreement with data reported by (Veronesi et al. 2015, Theriogenology 84:791–796) in dead puppies, and suggests the important role of C around the time of birth. However the exact source of the C accumulated in claws of puppies at birth must be clarified, while the source of C accumulated at 30, and even more at 60 days, can be supposed to be addressed to the newborn itself.