Background: The Charlson index is a widely used measure of comorbidity. The objective was to compare Charlson index scores calculated using administrative data to those calculated using case-note review (CNR) in relation to all-cause mortality and initiation of renal replacement therapy (RRT) in the Grampian Laboratory Outcomes Mortality and Morbidity Study (GLOMMS-1) chronic kidney disease cohort. Methods: Modified Charlson index scores were calculated using both data sources in the GLOMMS-1 cohort. Agreement between scores was assessed using the weighted Kappa. The association with outcomes was assessed using Poisson regression, and the performance of each was compared using net reclassification improvement. Results: Of 3382 individuals, median age 78.5 years, 56% female, there was moderate agreement between scores derived from the two data sources (weighted kappa 0.41). Both scores were associated with mortality independent of a number of confounding factors. Administrative data Charlson scores were more strongly associated with death than CNR scores using net reclassification improvement. Neither score was associated with commencing RRT. Conclusion: Despite only moderate agreement, modified Charlson index scores from both data sources were associated with mortality. Neither was associated with commencing RRT. Administrative data compared favourably and may be superior to CNR when used in the Charlson index to predict mortality.