In June 2008, the Cedar River crested flooding more than 5,000 Cedar Rapids homes. Residents whose homes were flooded were invited to participate in this study. We characterized exposures and symptoms experienced by individuals inhabiting 73 flood-damaged homes. Exposures and questionnaire-based health assessments were compared at two levels of remediation, in-progress and completed. Homes with remediation in-progress (n=24), as compared to the completed homes (n=49), had significantly higher airborne concentrations of mold, bacteria, iPM, endotoxin and glucan. Residents of in-progress homes had a significantly higher prevalence of doctor diagnosed allergies (adjusted OR=3.08; 95%CI: 1.05-9.02) and all residents had elevated prevalence of self-reported wheeze (adjusted OR=3.77; 95%CI: 2.06-6.92) and prescription medication use for breathing problems (adjusted OR=1.38; 95%CI: 1.01-1.88) after the flood as compared to before. Proper post-flood remediation led to improved air quality and lower exposures among residents living in flooded homes. Recognition of endotoxin as a proinflammatory ligand for pattern recognition receptors has increased the demand for endotoxin assessment in studies of environmental lung disease. Measurements using the Limulus amebocyte lysate (LAL) assay of air and reservoir dust samples are routinely incorporated into epidemiologic studies. However, it is unknown if endotoxin reactivity in the LAL assay varies by its physical presentation as aggregates, as membrane components of whole bacteria or as shed membrane blebs or if this parallels differences in the inflammatory potency of endotoxin in vivo. Endotoxins as14C-labeled-lipooligosaccharide (14C-LOS) and 14C- labeled-lipopolysaccharide (14C-LPS) were produced from Neisseria meningitidis and Escherichia coli. The reactivity of the endotoxin presentations was assessed in the LAL assay and in vivo using a murine model. The LAL assay significantly underestimated the quantity of endotoxin in the whole bacteria form whereas there was no significant difference in detecting endotoxin in aggregate and bleb forms. The failure of the LAL assay to equally quantify endotoxin was not mirrored in vivo where all three presentations of endotoxin were equally inflammatory. The inability of the LAL assay to detect the full quantity of endotoxin presented in the whole bacteria form has troubling implications for exposure assessment studies. Various extraction methods were applied to samples of known endotoxin quantity to improve the detection ability of the LAL assay. Extraction using EDTA and Tris/EDTA significantly improved the detection of endotoxin compared to the reference method of extracting in pyrogen-free water. These extraction methods also significantly increased the quantity of endotoxin measured in house and barn dust samples. A higher quantity of endotoxin measured in the LAL assay corresponded to a higher neutrophilic response in vivo. A standardized methodology for endotoxin detection that mimics the in vivo response is necessary for accurate and consistent endotoxin analysis.