Objectives This study evaluates the agreement of data on dental caries between electronic dental records and data retrieved from the national SKaPa-registry (Swedish Quality Registry for caries and periodontal disease), with special reference to e/M in deft/DMFT. Methods In a random sample of 500 6- and 12-year-old children having received dental care in 2014 in the county region of Värmland, Sweden, the diagnostic accuracy of data in electronic dental records with corresponding data obtained from the SKaPa-registry was compared by using Cohen’s Kappa and Intraclass correlation coefficient (ICC). Results For dft/DFT the Kappa was 0.95, and ICC 0.98 (total population). For deft/DMFT in the total population the Kappa was 0.80 and ICC 0.96. For 6-year-olds (deft) the Kappa was 0.89 and ICC 0.99 and for 12-year-olds (DMFT) the Kappa was 0.70, and ICC 0.83. The corresponding figures for Kappa and ICC when excluding individuals without caries (deft/DMFT = 0) were: Total population 0.63 and 0.94; 6-year-olds 0.79 and 0.99; 12-year-olds 0.42 and 0.68. Conclusion Agreement between data in the dental records and SKaPa was very high for dft/DFT confirming that transfer from the dental records to the SKaPa-registry is safe and correct. As the accuracy of deft/DMFT was considerably lower than for dft/DFT we advise against using deft/DMFT data from SKaPa for research purposes at this point.