The hygiene hypothesis of asthma and allergy has recently received a swell of popularity and published supporting evidence, and has been extended to autoimmune conditions of childhood. Broadly stated, naturally occurring infections and microbial exposures might essentially immunize against the development of asthma and allergic and autoimmune diseases. If true, then reductions in nature's immunotherapy over the past century might be a major factor in the global increase of these conditions (eg, the higher prevalence of asthma and allergies in urban metropolitan areas compared with rural and farm communities) and might lead to new therapies for these conditions. Although such a unifying hypothesis has great appeal, currently it is only speculation about what might be at the end of the investigative road. How close are the current studies to establishing a causal relationship between microbial exposures and a reduction in allergic, asthmatic, and autoimmune disease prevalence? A systematic epidemiologic appraisal of the current hygiene hypothesis evidence can provide a critical analysis of what is currently known and an investigative blueprint for future studies that can ultimately prove causation and improve recommendations, interventions, and therapies.