Pathogenic bacteria use a variety of ways to infect human hosts and cause disease. Bacterial pathogens produce a number of molecules that bind to host cell targets, allowing them to support a variety of host responses. Bacterial molecular mechanisms for interacting with the host might be unique to certain pathogens or conserved across multiple species. The underlying causes set in motion the pathogenic mechanisms of a disease (or condition), which if regulated would allow the disease to be averted. Epidemiological observations are frequently used to identify a potential cause before a pathological link between the cause and the disease can be established. In the interdisciplinary topic of molecular pathological epidemiology, the pathological perspective can be immediately integrated into an epidemiological approach. By correlating a putative risk factor to molecular pathologic markers of a disease, molecular pathological epidemiology can aid in determining aetiology and causality. As a result, the molecular pathological epidemiology paradigm has the potential to enhance the field of causal inference.