Abstract Background People with higher socio-economic status (SES) are generally in better health. Less is known about when these socio-economic health differences set in during childhood and how they develop over time. The goal of this study was to prospectively study the development of socio-economic health differences in the Netherlands, and to investigate possible explanations for socio-economic variation in childhood health. Methods Data from the Dutch Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort study were used for the analyses. The PIAMA study followed 3,963 Dutch children during their first eight years of life. Common childhood health problems (i.e. eczema, asthma symptoms, general health, frequent respiratory infections, overweight, and obesity) were assessed annually using questionnaires. Maternal educational level was used to indicate SES. Possible explanatory lifestyle determinants (breastfeeding, smoking during pregnancy, smoking during the first three months, and day-care centre attendance) and biological determinants (maternal age at birth, birthweight, and older siblings) were analysed using generalized estimating equations. Results This study shows that socio-economic differences in a broad range of health problems are already present early in life, and persist during childhood. Children from families with low socio-economic backgrounds experience more asthma symptoms (odds ratio (OR) 1.27; 95% Confidence Interval (CI) 1.08-1.49), poorer general health (OR 1.36; 95% CI 1.16-1.60), more frequent respiratory infections (OR 1.57; 95% CI 1.35-1.83), more overweight (OR 1.42; 95% CI 1.16-1.73), and more obesity (OR 2.82; 95% CI 1.80-4.41). The most important contributors to the observed childhood socio-economic health disparities are socio-economic differences in maternal age at birth, breastfeeding, and day-care centre attendance. Conclusions Socio-economic health disparities already occur very early in life. Socio-economic disadvantage takes its toll on child health ...