Variations in data collection between collecting regions can affect the outcome measures. This study examines the impact of improvements in data collection on outcome measures in a national monitoring programme between 2007/2008 and 2010/2011. Multilevel analysis of 2007/2008 and 2010/2011 National Child Measurement Programme (NCMP) data estimated the relationship between body mass index (BMI) z-score and data collection variations within coordinating regions, while adjusting for individual-level and school-level factors. The total sample was 2,013,285 students from 17,279 primary schools in 152 coordinating regions in England. Data collection differences accounted for 31.2% of the regional variation in BMI z-score for Reception (aged 4-5 years) students in 2007/2008; this reduced to 12.6% in 2010/2011. For Year 6 (aged 10-11 years) students, it reduced from 5.3% in 2007/2008 to 2.4% in 2010/2011. Digit preference in the rounding of weight measurements showed the largest decreases, from 27.3 to 4.5% for Reception year pupils and from 4.2 to 1.0% for Year 6 pupils. This demonstrates that improvements in data collection variation between regions in the NCMP have led to improvements in data quality.