A portable and robust system which is suitable for the automated analysis of DNA or RNA of selected pathogens such as foot-and-mouth disease virus (FMDV) is developed. The system incorporates a stationary PCR chip and is coupled with a DNA chip and an electrical detection for the sequence-specific identification of the PCR products. The PCR chip represents a miniaturized form of the classical thermocyclers and enables a fast and sensitive amplification as well as labeling of specific DNA sequences with minimal space and energy requirements. The detection and identification of the PCR products is performed on a DNA chip with an electrical detection scheme. The combination of the two technologies allows a very fast and highly specific sequence-based detection and differentiation of pathogens. Further, it combines the accuracy of sequence analysis with the speed of chip technologies. For the total analysis including DNA amplification and DNA detection, less than 2 h are required.