Background: Understanding how comorbidity measures contribute to patient mortality are essential both to describe patient health status and to adjust for risks and potential confounding. The Charlson and Elixhauser comorbidity indices are well-established for risk adjustment and mortality prediction. Still, a different set of comorbidity weights might improve the prediction of in-hospital mortality. The present study, therefore, aimed to derive a set of new population-based Elixhauser comorbidity weightings, to validate and compare them against those of the Charlson and Elixhauser-based van Walraven weightings in an adult in-patient population-based cohort of general hospitals. Methods: Retrospective analysis was conducted with routine data of 102 Swiss general hospitals (2012–2017) for 6.09 million inpatient cases. To derive the population-based weightings for the Elixhauser comorbidity index, we randomly halved the inpatient data and validated the results of part 1 alongside the established weighting systems in part 2, to predict in-hospital mortality. Charlson and van Walraven weightings were applied to Charlson and Elixhauser comorbidity indices. Derivation and validation of weightings were conducted with generalized additive models adjusted for age, gender and hospital types. Results: Overall, the population-based weights’ c-statistic (0.867, 95% CI: 0.865–0.868) was consistently, yet minimally higher than Elixhauser-van Walraven’s (0.863, 95% CI: 0.862-0.864) and Charlson’s (0.850, 95% CI: 0.849–0.851) in the derivation and validation groups. The net reclassification improvement of new weights improved the predictive performance by 1.6% on the Elixhauser-van Walraven and 4.9% on the Charlson weightings.Conclusions: All weightings confirmed previous results with the national dataset. The new population-based weightings model improved slightly the prediction of in-hospital mortality in Swiss hospitals. The newly derive weights support patient population-based analysis of in-hospital mortality and seek country or specific cohort-based weightings.