This article explores the impact of the post-socialist transformation of Czech society on the health of newborns from different socioeconomic groups. We use six different measures of child health as dependent variables and the mother’s educational attainment as the key predictor. We used birth certificate data on all singleton births in selected years and estimated a series of random-intercept multi-level models. The analysis consistently showed large gaps in health between children born to mothers with elementary education on the one hand and all other children on the other hand. While the trends are not entirely congruent across all measures of child health, we find more evidence of growing inequality than of declining or stable inequality. Inequality grew most in the 1990s and then stabilised or even declined. We offer two tentative explanations for observed growth in inequality: the selective adjustment hypothesis and the selective childlessness hypothesis.