The nativity composition of the Taiwan population has changed substantially since 1980, which resulted in one in six children being born to foreign-born mothers in 2004. The purpose of this study was to compare the early neonatal mortality rates among babies of foreign-born and Taiwan-born mothers. Data was obtained from the Taiwan Birth Registry Database in 2004 by the Bureau of Health Promotion, Department of Health, Taiwan. Multivariate analysis was used to examine the influence of the different maternal nationalities on early neonatal mortality after adjusting for important maternal and infant variables. Infants born to foreign-born mothers had a lower early neonatal mortality rate (5.6 per thousand) compared to those born to Taiwan-born mothers (9.4 per thousand). Even after adjusting for important maternal and infant variables, newborns of foreign-born mothers still had a lower risk of early neonatal death compared to newborns of Taiwan-born mothers (odds ratio = 0.68, 95% CI = 0.57-0.80). Foreign-born status may serve as an important index of differentiation in early neonatal mortality among the current Taiwan population. Selection, economic and non-economic aspects may explain the paradox of favorable early neonatal mortality outcomes.