The objective of this study was to investigate the utilization of the diagnose-based Charlson Comorbidity Index (CCI) and the medication-based Rx-Risk Comorbidity Index on Swedish administrative data. Data was collected over a ten-year period from the National Patient Register and the National Prescribed Medication Register on 3609 respondents from the national public health survey 2018, aged 16-84 and registered in Stockholm County. The overall aim was to identify comorbid conditions in the study population; and to examine if the identified comorbidities differ between indices, based on subject characteristics such as age and gender. Moreover, the specific aim was to quantify correlation between the indices, as well as within indices over look-back periods of up to ten years. Among the study population, 13 % were identified with at least one comorbid condition through CCI, and 87 % had medications indicative of at least one condition covered by Rx-Risk. Both the original Charlson weights and updated weights by Quan were used to compute the comorbidity scores for CCI. Results showed that when CCI and Quan may have scored low, the Rx-Risk picked up more conditions. The Spearman rank correlation between CCI and Quan scores resulted in relatively high correlation with a coefficient of 0.82 (p-value < 0.05) over look-back periods of 2, 5 and 10 years. Moreover, the correlation between CCI and Rx-Risk was fairly low over all look-back periods with a correlation coefficient of 0.34 (p-value < 0.05) at most. The within-correlation showed that CCI identified much of the comorbidity between the one- and two-year look-back periods, whilst Rx-Risk identified much comorbidity within the one-year look-back period. The overall implications of the presented results are that a utilization of Charlson index and Rx-Risk is likely to capture comorbid conditions in different health care settings, and thus expected correlation is to be of modest level between the two indices. The research question of interest should therefore determine which index is favorable when assessment of comorbidity is desired.