Abstract Background Health professionals, policy-makers and researchers need to be able to explore potential associations between prevalence rates and quality of care with a range of possible determinants including socio-economic deprivation and morbidity levels to determine the impact of commissioning and service delivery. In the UK, data in England are only available nationally at practice postcode level. In Scotland, such data are available based on an aggregate of the practices population's postcodes. The use of data assigned to the practice postcode may underestimate the association between ill health and income deprivation. Here, we report on the impact of using data assigned to the practice population by comparing analyses using English and Scottish data. Results Income deprivation based on data assigned to the practice postcode under-estimated deprivation compared to using income deprivation data assigned to the practice population for the five least deprived deciles, and over-estimated deprivation for the five most deprived deciles. The biggest differences were found for the most deprived decile. A similar trend was found for limiting long-term illness (LLTI). Differences between the QOF prevalence rates of the least and most deprived deciles using practice postcode data were similar (0.2% points or less) in England and Scotland for 8 out of 10 clinical domains. Using practice population assigned deprivation, differences in the prevalence rate between the least and most deprived deciles increase for all clinical domains. A similar trend was again found for LLTI. Using practice population assigned deprivation, differences for population achievement increase for all CHD quality indicators with the exception of beta-blockers (CHD10). With practice postcode assigned deprivation, significant differences between the least and most deprived deciles were found for 2 out 8 indicators, compared to 5 using practice population assigned deprivation. For LLTI differences between the lowest and most deprived deciles increased for all indicators when ill health assigned to the practice population was used. Conclusion We have found, through comparing deprivation and ill health data assigned to either the practice postcode or the practice population postcode in Scotland, that analyses based on practice postcode assigned data under-estimated the relationship between deprivation and ill health for both prevalence and quality care. Given the importance of understanding the effect of deprivation and ill health on a range of determinants related to health care, policy makers should ensure that practice population data are available and used at national level in England and elsewhere where possible.