Large-scale historical databases featuring individual-level causes of death offer the potential for longitudinal studies of health and illnesses. There is, however, a risk that the transformation of the primary sources into ‘data’ may strip them of the very qualities required for proper medical historical analysis. Based on a pilot study of all 11,100 deaths registered in Copenhagen in 1880–1881, we identify, analyse and discuss the challenges of transcribing and coding cause of death sources into a database. The results will guide us in building Link-Lives, a database featuring close to all nine million Danish deaths from 1787 to 1968. The main challenge is how to accommodate different older medical rationales in one classification system. Our key finding is multi-coding with more than one version of the ICD system (e.g. ICD-1893 and ICD-10) can be used as a novel method to systematically handle historical causes of death over time.