Background: Dramatic social changes took place in the Baltic States (Estonia, Latvia and Lithuania) in the 1990s. This study investigates the extent to which social variations in self-assessed health changed during that period. Methods: Norbalt Living Conditions Survey I (1994) and II (1999) random population-based samples in Estonia, Latvia and Lithuania were analysed. Associations of self-assessed health with six social dimensions (education, economic activity, car ownership, number of rooms, ethnicity and residence) were studied for males and females aged 25–74 years (n = 16?970). Results: Substantial and significant associations with poor health were found for education, economic activity, car ownership and, to a lesser extent, number of rooms. Ethnic differences were found only among women in Estonia. By and large, social variations in health were comparable for most indicators between the three countries. Differences in self-assessed health were stable between 1994 and 1999, except for the relatively worse position of the economically non-active in 1999. Conclusions: Substantial social inequalities in self-assessed poor health exist in the Baltic States. Despite dramatic social changes taking place, social variations in self-assessed health have been rather stable in the second half of the 1990s. The economically non-active seem to have become more disadvantaged.