The drinking water and wastewater industries are interested in developing a better understanding of sources of fecal contamination. Microbial source tracking (MST) offers the potential to apportion the contribution of various animal groups to this contamination. However, while there are many methods available there is no clear indication as to the most appropriate approach. There has been little systematic comparison of methods and only a few blind trials, and issues of reproducibility, accuracy, sensitivity, specificity, resolution, and robustness need to be addressed. There is confusion among potential end-users and some disagreement among scientists. Therefore, due to the uncertainty surrounding the most appropriate tools and applications of MST, a workshop of 45 experts representing water and wastewater utilities, academia, state and federal government agencies, medical institutions, and private laboratories was convened in San Antonio, Texas over a three-day period (February 16 – 18, 2005). The overall objective of the workshop was to identify the knowledge gaps and research needs for application of MST technologies by the wastewater and drinking water industries.