Rapid-cycle real-time polymerase chain reaction (PCR) methods may revolutionize the manner in which plant pathogens are identified and diseases are diagnosed. As the genomics age progresses and more and more DNA sequence data become available, highly specific primers and fluorescent probe sequences can be designed to yield target amplicons to unique regions of a pathogen's genome. Portable real-time PCR instruments described here are now allowing for diagnostic assays to be run directly in the field or at remote locations other than the standard diagnostic laboratory. Rapid real-time PCR diagnosis can result in appropriate control measures and (or) eradication procedures more quickly and accurately than traditional methods of pathogen isolation. Disease losses are minimized and control costs reduced. Advantages and disadvantages of rapid real-time PCR for the detection of bacterial, fungal, and viral plant pathogens are described.