Background: An important gap in our knowledge of social inequalities in health is the former Yugoslavia, a region of culturally and historically diverse countries, with recent conflict. The aim of the present paper is to investigate relative and absolute inequalities in self-assessed health in former Yugoslavia (Bosnia-Herzegovina, Croatia, Kosovo, Macedonia, Montenegro, Slovenia and Serbia) by sex and education. Methods: The data source is the South-East European Social Survey Project fielded in December 2003 to Winter 2004, covering the former Yugoslavia with a total sample of 18 481 respondents. Data from Slovenia were obtained from the 2004-wave of the European Social Survey. The health outcome variables were self-reported general health (SRH) and limiting longstanding illness (LLI). Results: Both absolute and relative educational health inequalities were present throughout the former Yugoslavia to a larger or lesser extent, although odds ratios (ORs) for LLI and SRH were not significant for Montenegrin women [LLI OR = 1.12, 95 confidence interval (CI): 0.92-1.37; SRH OR = 1.16, 95 CI: 0.96-1.40] and with respect to the reporting of LLI among Slovenian men (OR = 1.16, 95 CI: 0.96-1.44). Overall, Montenegro held the best position. Conclusions: The prevalence of poor health and the degree of relative inequality in self-assessed health in the former Yugoslavian countries were similar in order to one another, and to other East European countries during the same period. Influences on subjective health require further elucidation. Further research should study a wider range of health outcomes using larger survey samples and a wider range of cultural and other predictor variables.