The identification of impurities with mutagenic potential is required for any potential pharmaceutical. The ICH M7 guidelines state that two complementary in silico toxicity prediction tools may be used to predict the mutagenic potential of pharmaceutical impurities. An expert review of the resulting in silico predictions is required, and numerous publications have been released to guide the expert review process. One such publication suggests that literature-based structural alerts (LBSAs) may provide a suitable aid in the expert review process. This publication provides a study of the effect of using one such set of LBSAs for the expert review of mutagenicity predictions from two complementary in silico tools. The analysis was performed using an Ames test dataset of 2619 compounds, and required interpretation of the LBSAs which proved to be a subjective process. Globally the LBSAs produced many more false positives than the in silico systems; whilst some exhibited a predictive performance comparable to the in silico systems, the majority were overly sensitive at the cost of accuracy. Use of LBSAs as part of an expert review process, without considering mitigating factors, could result in many more false positives and potentially the need to carry out additional and unnecessary Ames tests.