Pioneering bench researchers describe in detail the cutting-edge techniques they have developed for analyzing the genomes and gene products in a diverse range of protozoan and metazoan parasites. These readily reproducible techniques can be used in genomic, functional genomic, and post-genomic studies and include transfection methods and vectors for several protozoan parasites, global analysis using microarrays, gene ablation using RNA interference, gene knockout, mutagenesis, and chromosome manipulation. Some of the protocols require DNA sequence data, whereas others were developed independently of whole-genome sequence data. The protocols presented follow the successful Methods in Molecular Biology series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and the avoidance of known pitfalls.