Based on a new mathematical model of differential display (DD), this updated second edition takes advantage of automation, as well as digital data acquisition and analysis. The authors explain and highlight all the recent methodological refinements, including automated liquid handling of hundreds of DD PCR reaction setups combined with capillary electrophoresis, a prototype computer program to automatically allow positive band identification from a fluorescence differential display (FD) image, and restriction fragment-based DD screenings. Other improvements discussed are the combining of DD and DNA microarrays by reducing the complexity of cDNA probes while increasing the sensitivity of detection, and a DD approach to detect prokaryotic mRNA expression. The authors also demonstrate the power of DD technology with a collection of outstanding examples of DD applications and detailed experimental procedures. The elegant studies described here have led to the discovery of many important genes involved in viral infection, Prion disease, cancer, ovulation, circadian clock, floral color, transcription repression gene silencing, mRNA polymorphism, and protein-RNA interaction.