Most diseases are “complex” in that they are caused by the joint action of multiple genetic and environmental (including lifestyle) factors, playing out over age and time. The most interesting etiologic questions for complex diseases bear on possibly shared pathways, co-regulated families of genes and the mechanisms by which genetic and environmental factors modulate specific biologic processes. Methods to characterize joint effects on susceptibility to complex diseases should ideally illuminate the causal processes themselves, at mechanistic levels of understanding.