Important advances in the understanding of gene structure, function and regulation have advanced the field of mutation analysis beyond recognition in a very short space of time. Much of this has been through the analysis and manipulation of nucleic acids using gene cloning and DNA sequencing. This has been accelerated through the discovery of DNA-manipulating enzymes, such as DNA polymerase, DNA ligase and reverse transcriptase. In particular, restriction endonucleases provided not only a turning point for the analysis of DNA but also the means to develop recombinant DNA technology as well as key methods for gene library production, molecular cloning and DNA sequencing. This chapter provides the detail of the techniques of cDNA and genomic library production and the identification of specific DNA fragments. In addition the key technology of DNA sequencing, which has allowed the development of the field of genomics, is presented, together with an overview of the newer technologies of second- and third-generation sequencing.