The last decade has seen diverse pathogens such as Cryptosporidium parvum and toxigenic Escherichia coli O157 rise to prominence within the water industry. In addition, many potentially waterborne pathogens have been identified as possible problems. These emerging pathogens include various species of microsporidia, the Mycobacterium avium complex of bacteria, Helicobacter pylori, and enteric viruses, among many others. The same time period has witnessed a revolution in molecular biology and the application of molecular tools such as the polymerase chain reaction (PCR) to many organisms that concern the water industry. These techniques have greatly advanced the science of microbiology and are providing valuable information that will improve many aspects of microbiological water quality. As populations continue to grow and the demand on water resources increases, the water industry is going to need an ever improving toolbox with which to ensure the microbiological quality of drinking water. This paper describes many of the applications of molecular tools to drinking water microbiology with particular reference to Cryptosporidium, Giardia, and E. coli O157, and speculates on the new horizons in drinking water quality that may be addressed by the application of molecular technology. Includes 23 references.