The Invader technology has been developed for the detection of nucleic acids. It is a signal amplification system able to accurately quantify DNA and RNA targets with high sensitivity. Exquisite specificity is achieved by combining hybridization with enzyme recognition, which provides the ability to discriminate mutant from wild-type at ratios greater than 1/1000 (mutant/wt). The technology is isothermal and flexible and incorporates a homogeneous fluorescence readout. It is therefore readily adaptable for use in clinical reference laboratories, as well as high-throughput applications using 96-, 384-, and 1,536-well microtiter plate formats. The molecular mechanism of the system and specific applications for use in clinical and research laboratories are described. These include direct analysis of unamplified human genomic DNA to detect mutations and single-nucleotide polymorphisms associated with factor V Leiden, factor II, cystic fibrosis, and apolipoprotein E, and gene expression assays that quantify messenger RNA levels in cells using direct lysates.