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We compared perinatal mortality rates (PMRs) and the risk from certain causes among immigrant and native population in the Valencian Community (Spain). Using data from the Perinatal Mortality Registry, crude and age standardized mortality ratios were obtained in the different groups of mothers. Mortality rate ratios were calculated to compare the causes of death resulting from prematurity, congenital anomalies, infectious diseases and Sudden Infant Death Syndrome between Spanish and foreign women. PMRs were higher among all the immigrant groups compared with the native population, with a statistical significance in Eastern European and sub-Saharan mothers. Neonatal mortality rates in North African and Latin American mothers were similar to those of native women. Babies of immigrant mothers were at a significant higher risk of dying from late infectious diseases and from causes resulting from being premature. More research is needed on the risk factors which contribute to generating differences in our setting.