Endotoxin has been found to be a contaminant in human in vitro fertilization (IVF), leading to low pregnancy rates, mostly through embryo fragmentation. We wished to determine if standard quality control assays (one-cell and two-cell mouse embryo culture) were able to detect the presence of endotoxin and how they compared with the zona-free mouse embryo assays. Endotoxin was detected by the zona-free mouse embryo assays but not by the one- or two-cell mouse embryo assays. When excessive embryo fragmentation is noticed in the human IVF system, the use of zona-free mouse embryo assays is recommended.