Terminal Restriction Fragment (TRF) patterns, also known as Terminal Restriction Fragment Length Polymorphisms (T-RFLP), are a recently introduced PCR-based tool for studying microbial community structure and dynamics. Since the first review of TRF methodology (Marsh, 1999. Curr. Op. Microbiol. 2: 323-7), at least 35 new research articles were published that include this powerful tool in some part of their reports. This review covers some of the applications that TRF patterns were used for and provides a discussion of how to create and analyze TRF pattern data. This data has the advantage of being simply and rapidly produced using standard DNA sequencing equipment. The raw data are automatically converted to a digitized form that can be easily analyzed with a variety of multivariate statistical techniques. The identification of specific elements in a TRF pattern is possible by comparison to entries in a good sequence database or by comparison to a clone library. As an added advantage when investigating complex microbial communities such as those in soils and intestines, TRF patterns are recognized as having better resolution than other DNA-based methods for evaluating community structure.