Pathogen recognition is a central activity of the Toll-like receptor (TLR) family. Molecules from various pathogens have been widely used in TLR research as natural ligands for the receptors. TLR ligands from bacteria, viruses, and fungi are widely available from commercial companies and are increasingly being manufactured with high purity specifically for use in TLR research. Although increasingly used in TLR research, extracts from many parasites with potential TLR ligands are not generally produced commercially. Historically, parasite extracts were produced in academic laboratories for diagnostic or vaccination research, often without an emphasis on quality control. Here we describe methods for isolation of eggs from the human parasite Schistosoma mansoni . We also describe a protocol for generation of S. mansoni soluble egg antigens (SEA), which are commonly used in TLR research. This protocol has application for the isolation of extract from other parasites or pathogens as it is intended to reduce contamination that may cause spurious data in TLR research.