Pyrosequencing technology allows to determine short DNA sequences (100–150 b. p.) that meets the demands of SNP assessment and mutation detection. This is a newly developed non-electrophoretic method based on sequencing by synthesis and relies on real-time quantification of phosphate release during DNA synthesis. Systems for automated pyrosequencing reactions enable analysis of more than 1,000 samples per 24 hours in a single machine. It can be used in routine clinical practice for rapid identification of infectious agents and inherited predisposition for complex disease and individual drug responses.