Molecular biology methods such as PCR and hybridization have significantly decreased the length of time required for the detection of waterborne pathogens. For some waterborne agents like noroviruses, PCR and hybridization assays are the only reliable methods for their detection. The advantages gained by PCR have introduced new problems for applying these assays to detect waterborne pathogens. These problems include, but are not limited to: sample carryover contamination, difficulty in detecting potentially viable agents, and the difficulty in optimizing an assay to detect more than 1 pathogen or gene target per reaction. Gene chip technology is now being widely reported as the solution for overcoming some of these shortfalls. The authors' research that is presented in this paper highlights both the benefits and drawbacks of using this relatively new molecular biology technique. It concludes with several recommendations on how this method might be improved so that it becomes a more robust assay system in terms of speed, specificity and sensitivity and easier for end users to perform. Includes 17 references, figures.