Advances in the basic science technologies (monoclonal antibodies, polymerase chain reaction, and molecular genetic techniques) have lead to more sensitive and specific detection systems for gastrointestinal pathogens. In the past year, two different monoclonal-based, enzyme-linked immunosorbent assays have been described that specifically detect pathogenic Entamoeba histolytica in stool. A number of different pretreatment methods have been employed to improve polymerase chain reaction detection of pathogens in stool. Two studies have used immunomagnetic beads (ie, monoclonal antibody-coated) to selectively isolate salmonellae and shigellae followed by detection using polymerase chain reaction-based tests. Spin column chromatography isolation of Norwalk virus allowed for rapid detection of this virus by reverse transcriptase-polymerase chain reaction. A Quiagen procedure improved detection of the toxin A gene target for direct detection of Clostridium difficile by polymerase chain reaction methods. Results of recent evaluations of new commercially available products for detection of Cryptosporidium spp are evaluated. This report emphasizes tests with improved sensitivity, specificity, and utility in the clinical microbiology laboratory.