Background: A growing number of children live in single-parent families, which seems to be associated with negative effects on a child’s health. Little is known about the health of children in cohabiting two-parent families that are also increasingly common, and more susceptible to family break-up than married two-parent families. This study seeks to determine if family type is associated with child mortality and whether any association remains after controlling for socio-economic factors. Methods: We used longitudinal nationally representative register data from Statistics Finland to study deaths between ages 1–14 years (1780 deaths, N = 201 211) during 1990–2004. The relative effects of family characteristics on mortality were estimated using Cox regression models. Results: Compared with children of married parents, children of single parents carried an excess risk in mortality in ages 1–4 years [Hazard Ratio (HR) 2.02, 95% CI 1.63–2.51] and in ages 5–9 years (HR 1.44, 95% CI 1.15–1.80). The relationship between single parenthood and mortality was largely, but not entirely, explained by associated low parental education and lower household income. Mortality among children in cohabiting-parent families showed no difference from children of married parents. Conclusion: Mainly due to accidental and violent causes of death, the largest excess mortality risks concentrated among children of single, less-educated and less-earning parents. The most vulnerable age period in this respect was early childhood (ages 1–4 years), whereas no association between mortality and family type was found among children aged 10–14 years.