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Background/Objectives Erythema toxicum neonatorum (ETN) and transient neonatal pustular melanosis (TNPM) are benign pustular skin conditions that are relatively common in newborns, but the predisposing factors for these conditions are unknown. Our goal was to verify the prevalence of ETN and TNPM and their predisposing factors in a large sample of neonates. Methods In this prospective 1-year multicenter study, 2,831 neonates (age ≤72 hours) born in southern Brazil were randomized to undergo skin examination by a dermatologist. Results Most were Caucasian (of European descent). There were 602 cases of ETN (21.3% prevalence) and 97 cases of TNPM (3.4% prevalence). ETN was more prevalent in Caucasian neonates, male neonates, those with 1-minute Apgar scores from 8 to 10, those who had no gestational risk factors, and those not admitted to a neonatal intensive care unit (NICU). Positive correlations were observed between ETN and gestational age and birthweight. ETN was least frequent in the winter. No NICU admission or birth during the spring was associated with TNPM. Conclusions At least in the region where this study was conducted, seasonality affects these benign pustular skin conditions. The health of the child at birth, gestational age, and birthweight influenced the development of ETN. This finding may indicate a role of immune system maturity in ETN, but additional studies are needed to confirm this.