BACKGROUND: Early diagnosis of chronic kidney disease (CKD) facilitates best management in primary care. Testing coverage of those at risk and translation into subsequent diagnostic coding will impact on observed CKD prevalence. Using initial data from 915 general practitioner (GP) practices taking part in a UK national audit, we seek to apply appropriate methods to identify outlying practices in terms of CKD stages 3-5 prevalence and diagnostic coding. METHODS: We estimate expected numbers of CKD stages 3-5 cases in each practice, adjusted for key practice characteristics, and further inflate the control limits to account for overdispersion related to unobserved factors (including unobserved risk factors for CKD, and between-practice differences in coding and testing). RESULTS: GP practice prevalence of coded CKD stages 3-5 ranges from 0.04 to 7.8%. Practices differ considerably in coding of CKD in individuals where CKD is indicated following testing (ranging from 0 to 97% of those with and glomerular filtration rate  <60 mL/min/1.73 m 2 ). After adjusting for risk factors and overdispersion, the number of  'extreme' practices is reduced from 29 to 2.6% for the low-coded CKD prevalence outcome, from 21 to 1% for high-uncoded CKD stage and from 22 to 2.4% for low total (coded and uncoded) CKD prevalence. Thirty-one practices are identified as outliers for at least one of these outcomes. These can then be categorized into practices needing to address testing, coding or data storage/transfer issues. CONCLUSIONS: GP practice prevalence of coded CKD shows wide variation. Accounting for overdispersion is crucial in providing useful information about outlying practices for CKD prevalence.