Exposures to fungi have been linked with asthma, toxicoses, hypersensitivity pneumonitis, and a range of non-specific symptoms. Definitive associations between indoor fungal exposure and health effects in population-based exposure-response studies, however, have not been well established. Issues in exposure assessment methods, both in collection and analysis, are major limitations. Classic methods for assessing airborne fungi rely upon collecting and analyzing whole fungal spores by culture. However, quantifying whole fungal spores may not fully describe fungal exposures, especially for purposes of investigating adverse respiratory health effects. New sampling methodologies and analytical techniques need to be developed that would more accurately characterize bioaerosol exposures. The recent Institute of Medicine report on "Damp Indoor Spaces and Health" recommends that exposure assessment for fungi should focus on non-culture techniques and that research on measurement of fungal constituents is important. Better characterization of fungal bioaerosol exposures would allow more successful detection of associations between fungal exposures and health effects. In the long-term, stronger and more definitive evidence of these associations should lead to earlier recognition and acknowledgment of building-related diseases by employers and in improved practices of building preventative maintenance and remediation by building owners.