Denaturing gradient gel electrophoresis (DGGE) is a molecular technique for fingerprint analysis of microbial community composition, diversity, and dynamics. The method is rapid and affordable, allowing multiple samples to be processed simultaneously. This protocol provides a background to the theory and progress in DGGE techniques and offers a detailed step-by-step procedure for laboratories employing DGGE for the analysis of microbial communities from environmental samples. Potential sources of bias are highlighted, in addition to a detailed troubleshooting section that helps overcome common problems. The protocol outlines steps for preparing gel solutions, pouring gels, operating the C.B.S. Scientific and Bio-Rad systems, and excising fingerprint bands for sequencing. All required reagents and supplies are listed, as are the sequences of the most commonly used PCR primers for DGGE of bacterial, archaeal, and eukaryotic 16S rRNA gene amplicons.