Background Many risk factors, such as smoking, affect multiple diseases. Calculating a disability-adjusted life-year (DALY) for such risk factors should take comorbidity into account. We aim to provide a tool for such calculations, using a counterfactual approach. Methods We defined a DALY in the original terms as a metric “to quantify loss of healthy years of life due to dying prematurely or to living with the health consequences of diseases, injuries or risk factors”, rather than use its operational form (the sum of healthy years lost through mortality and through disease). As a DALY reflects the effect of risk factor exposure in a particular year only, we calculate this by comparing future population health in the current situation and in the situation where the risk factor is absent in the particular year but returns to the value it would have had in the current situation after 1 year. We derived disability weights for comorbidity by multiplying (1 — disability weight) of the separate diseases. We also included disability weights greater than 0 for those without risk-factor-related disease, reflecting disability from all other diseases. We incorporated the calculation in the DYNAMO-HIA-2 programme, which implements a risk factor—disease Markov model. This reduces the computational burden on the user from entering the data. Findings Our method delivers a lower DALY than the WHO burden of disease approach, as the latter assumes that the years gained by elimination of the risk factor would all have been healthy years, while our method takes into account that part of these years would have been spent with disease. Interpretation The proposed method delivers a straightforward metric in terms of interpretation, fully taking competing mortality, morbidity, and comorbidity into account. However, handling of interaction effects (that is, those spared in one year are at risk in later years) needs further discussion. Funding This research was funded by the National Institute for Public Health and the Environment (RIVM) and partly by the Netherlands Organisation for Health Research and Development. The first version of DYNAMO-HIA was partly funded by the Directorate General for Health and Consumers of the European Commission.