Biomarkers are very useful tools when the metabolic fate of the compound or the etiology of a resultant disease is completely understood. They may contribute to confusion if it is not possible to distinguish between markers of exposure and markers of disease. Such is the case for biomarkers used in the assessment of diisocyanate exposure. Biomarkers for diisocyanate exposure result from both direct and indirect effects. Molecules such as hemoglobin, albumin, tubulin, glutathione, and laminin have been implicated as having been directly modified as a result of exposure to toluene diisocyanate (TDI). In addition, indirect biomarkers have included profiles of molecules such as antibodies, cytokines, cell accumulation or proliferation, and markers of oxidative stress. While a brief presentation of each of these markers is provided here, the focus is primarily on immunological markers as an example of the difficulties with using biomarkers in assessing diisocyanate exposure in general, and TDI specifically. Compiled data will be used to demonstrate where gaps exist in our understanding of how the results of measured biomarkers are used with regard to isocyanate exposure, and whether it may be possible to develop these tools to define thresholds between exposure and disease. Issues addressed include whether the marker represents a measure of exposure or disease, whether the methods are sufficiently uniform between labs to be able to compare between studies, and whether the ambiguities are the result of the complexity of the isocyanate reactivity in the biological system, or our inability to accurately measure the end point of the reactions.