This Working Group was assembled to review and evaluate methods currently used to estimate work site exposures to biological agents and to present recommendations on suitable measurement strategies. The current state of exposure assessment was evaluated for environments with organic dust including agriculture, composting, sewage and waste treatment processing, peat moss harvesting and handling, cotton and textile processing, greenhouse work, and grass seed processing. Methods for measurement of microbial contaminants in indoor environments were also considered. Important methods are emerging that use quantitative PCR for assessment of microbial agents. Difficulties exist with optimization of extraction to yield contaminant-free DNA without significant DNA loss. Advances in assays for microbial agents (e.g., endotoxin and glucans) as well as allergens have increased the utility of exposure assessment for these agents. A crucial area for further development is international harmonization of methodologies to reduce interlaboratory variability and to facilitate establishment of exposure guidelines. Endotoxin exposure assessment using the Limulus amebocyte lysate method is a high priority for harmonization because of its importance as a pulmonary inflammatory agent in many occupational settings.