Misidentification of cultured cell lines results in the generation of erroneous scientific data. Hence, it is very important to identify and eliminate cell lines with a different origin from that being claimed. Various methods, such as karyotyping and isozyme analysis, can be used to detect inter-species misidentification. However, these methods have proved of little value for identifying intra-species misidentification, and it will only be through the development and application of molecular biological approaches that this will become practical. Recently, the profiling of microsatellite variants has been validated as a means of detecting gene polymorphisms and has proved to be a simple and reliable method for identifying individual cell lines. Currently, the human cell lines provided by cell banks around the world are routinely authenticated by microsatellite polymorphism profiling. Unfortunately, this practice has not been widely adopted for mouse cells lines. Here we show that the profiling of microsatellite variants can be also applied to distinguish the commonly used mouse inbred strains and to determine the strain of origin of cultured cell lines. We found that approximately 4.2% of mouse cell lines have been misidentified; this is a similar rate of misidentification as detected in human cell lines. Although this approach cannot detect intra-strain misidentification, the profiling of microsatellite variants should be routinely carried out for all mouse cell lines to eliminate inter-strain misidentification.