BACKGROUND: Obesity is a significant public health issue. Obese children have an increased risk of developing chronic adult diseases. Knowledge of socio-economic distribution trends in childhood overweight/obesity is limited. METHODS: Body mass indices for 3-year-old children resident in three South Wales localities from 1995 to 2005 were derived from the National Community Child Health Database (NCCHD) and examined in relation to residence lower super output area (LSOA) Townsend Material Deprivation Score. RESULTS: Over 11 years, 53-69% of children had height/weight measurements recorded (with little difference observed across deprivation fifths). Amalgamating the data for all 11 years showed no significant association of prevalence with LSOA socio-economic status. Annual trends varied substantially: the most deprived fifth had the lowest proportion on five, and the highest on six, occasions. Linear regression analysis suggested a greater rate of increase of overweight/obesity in children from most-deprived LSOA areas compared with those from least deprived areas (not statistically significant). CONCLUSIONS: Socio-economic difference in overweight/obesity prevalence lessened between 1995 and 2005. Despite annual variation, this apparent closing of the gap has been the result of an increase in overweight/obesity prevalence in children from the most deprived areas who, initially, had a lower prevalence compared with children from least deprived areas, but by 2005, had overtaken them.