We describe the development of a single-primer amplification system, which uses the trypanosomal mobile genetic element RIME as a molecular marker for the differentiation of Trypanosoma brucei stocks. Using a well-characterised set of T brucei stocks from southeast Uganda, Kenya and Zambia, we have evaluated the application of this technique, termed MGE-PCR (mobile genetic element PCR) for the typing of trypanosome strains. The technique revealed considerable variation between stocks and was sufficiently specific to amplify trypanosomal DNA in the presence of host DNA. The results showed a clear distinction between human-infective and non-human-infective stocks. Comparative studies on these stocks using markers for the human serum resistance associated (SRA) gene, which identifies human-infective stocks, demonstrated complete agreement between MGE-PCR derived groups and human-infectivity status. Furthermore, MGE-PCR detects high levels of variability within the T. b. brucei and T. b. rhodesiense groups and is therefore a powerful discriminatory tool for tracking individual T. brucei genotypes and strains. (C) 2003 Elsevier Science (USA). All rights reserved.