Pulsed field gel electrophoresis (PFGE) has provided a very reliable system for separation of DNA fragments greater than 50 kb and has made a significant impact on the analysis of both prokaryotic and eukaryotic genomes. The chapters in this book cover both the theory behind this very important technique and present detailed protocols for many of its major uses. The first chapter describes the basis of PFGE with interesting new insights in modelling how PFGE separates large fragments of DNA. The next two describe the use of PFGE in constructing long range restriction site maps in mammalian genomic DNA and in the detection of gross rearrangements in the DNA of patients with Duchenne muscular dystrophy and Charcot-Marie-Tooth disease. There are four chapters dedicated to the use of PFGE in cloning form, construction of, analysis of, and transfer of yeast artificial chromosomes (YACs). The final two chapters describe the use of PFGE in the analysis of bacterial chromosomes and protozoan parasite chromosomes. This book will therefore be an essential resource book for researchers in laboratories that require PFGE in their research strategies, including those involved in molecular human genetics, mammalian genetics, molecular microbiology, molecular parasitology, biochemistry, and molecular diagnostics.