Detection of bacterial lipopolysaccharide (LPS) in the absence of overt infection is a challenging problem in tissue homogenates and other complex samples. We found that conventional Limulus amebocyte lysate (LAL) assays are not suitable for this purpose due to interference from beta-glucan-like molecules. In contrast, a modified LAL assay that is unaffected by beta-glucan-like molecules was able to detect LPS in infected tissue and in a subset of clinically aseptic tissues. A two-step LAL assay was used to exclude the possibility of false positives due to nonspecific amidases. False positives due to sample color were also excluded, as were false negatives due to assay inhibition. This is the first report to successfully detect LPS in tissue in the absence of overt infection. This approach may be extremely useful in assessing recent hypotheses that subclinical levels of bacteria contribute to a wide range of chronic diseases.