Current epidemiological and statistical theory about research methods and how to elicit causation from epidemiological studies is strongly influenced by counterfactual-manipulative thinking. However, thinking about how disease states develop is rooted in mechanistic ‘webs of causes’. After a tremendous growth of research in molecular biology, biochemistry and genetics, attention has increasingly been paid to environmental and socioeconomic factors as determinants of diseases. This led to conceiving of most pathologies as caused by multilevel mechanical systems. The nature of ‘mechanisms’ has been the subject of extensive philosophical reflection over the past couple of decades. The present paper will first present some of today's philosophical insights in what are called biologic or other ‘mechanisms’ and thereafter show how these concepts can be linked to counterfactual-manipulative views.