AIM: In this study from Quang Ninh province in northern Vietnam (sub-study of the trial Neonatal Health - Knowledge into Practice, NeoKIP, ISRCTN 44599712), we investigated determinants of neonatal mortality through a case-referent design, with special emphasis on socio-economic factors and health system utilization. METHODS: From July 2008 until December 2009, we included 183 neonatal mortality cases and 599 referents and their mothers were interviewed. RESULTS: Ethnicity was the main socio-economic determinant for neonatal mortality (OR 2.08, 95% CI 1.39-3.10, adjusted for mothers' education and household economic status). Health system utilization before and at delivery could partly explain the risk elevation, with an increased risk of neonatal mortality for mothers who did not attend antenatal care and who delivered at home (OR 4.79, 95% CI 2.98-7.71). However, even if mothers of an ethnic minority attended antenatal care or delivered at a health facility, the increased risk for this group was sustained. CONCLUSION: Our study demonstrates inequity in neonatal survival that is related to ethnicity rather than family economy or education level of the mother and highlights the need to include the ethnic dimension in the efforts to reduce neonatal mortality.