Plasmid extraction is typically performed to produce template DNA for a desired molecular biological reaction, or set of reactions, such as restriction endonuclease digestion (see Chapter 20), DNA sequencing (see Chapter 22), in vitro mutagenesis (see Chapters 23–26), transformation (see Chapters 4 and 5), transfection, or probe generation. The principal methodologies of extraction, involving either alkaline lysis or boiling are well established (1) and are described in detail in Chapters 8 and 9. These methods are relatively crude but are both inexpensive and rapid, and they yield DNA that is suitable for many molecular biology protocols. DNA of higher purity can be prepared using silica resin-based anion exchange as described in Chapter 10 or by separation on cesium chloride gradients (for details, see ref. 1, Chapter 1, Protocol 10). Plasmid minipreps are a ubiquitous part of molecular biology. They are simple and easy to perform but can be very tedious when large numbers of samples are involved. In recent years, endeavors such as the human genome project have led to the development of methods for the manageable high-throughput extraction of plasmids (2–15).