Sensitivity to a variety of fungi is known to be a factor in allergic rhinitis and asthma. In this review methods for measuring exposure to fungi in the indoor environment are evaluated. A variety of markers for the presence of fungi are also described in addition to their known relationship to either toxic or adverse immunologic effects. Key studies documenting the clinical effects of different types of fungi are also reviewed, as well as a description of abatement methods that either have been successful or need further investigation. Although many studies have shown an association between exposure to fungi and allergic disease, in many cases a direct cause-and-effect relationship has not been established. Improved knowledge of the epidemiology and mechanisms behind fungal-induced human disease will hopefully establish this causal link and suggest methods for reducing morbidity.