To determine the age and cause groups contributing to absolute and relative socio-economic inequalities in paediatric mortality, hospitalisation and tumour incidence over time. Deaths (n= 9559), hospitalisations (n= 834,932) and incident tumours (n= 4555) were obtained for five age groupings (<1, 1-4, 5-9, 10-14, 15-19 years) and four periods (1990-1993, 1994-1997, 1998-2001, 2002-2005) for Québec, Canada. Age- and cause-specific morbidity and mortality rates for males and females were calculated across socio-economic status decile based on a composite deprivation score for 89 urban communities. Absolute and relative measures of inequality were computed for each age and cause. Mortality and morbidity rates tended to decrease over time, as did absolute and relative socio-economic inequalities for most (but not all) causes and age groups, although precision was low. Socio-economic inequalities persisted in the last period and were greater on the absolute scale for mortality and hospitalisation in early childhood, and on the relative scale for mortality in adolescents. Four causes (respiratory, digestive, infectious, genito-urinary diseases) contributed to the majority of absolute inequality in hospitalisation (males 85%, females 98%). Inequalities were not pronounced for cause-specific mortality and not apparent for tumour incidence. Socio-economic inequalities in Québec tended to narrow for most but not all outcomes. Absolute socio-economic inequalities persisted for children <10 years, and several causes were responsible for the majority of inequality in hospitalisation. Public health policies and prevention programs aiming to reduce socio-economic inequalities in paediatric health should account for trends that differ across age and cause of disease.