The ability to type microorganisms to a sub-species level plays an essential role in the diagnosis, treatment and control of human infection. Traditionally, differentiation of microorganisms has involved analysis of phenotypic markers. However, these methods are not universally applicable to all microorganisms, and results may be influenced by environmental factors. Recent developments in DNA analysis, together with the limitations of phenotypic methods, have resulted in an increasing use of procedures based on DNA analysis for the typing of clinically important microorganisms. The aim of this review is to provide an overview of the advantages and disadvantages of the genetic typing techniques currently available.