African trypanosomes contain numerous variant surface glycoprotein (VSG) genes, but express only one at a time. When different VSG genes are activated by gene duplicative or non-duplicative mechanisms, antigenic variation occurs. Although transcriptionally inactive VSG genes can have either an intra-chromosomal or a telomeric location, all expressed VSG genes so far examined are telomeric. Some VSG genes are located on minichromosomes of approximately 100 kilobases (kb), but all those thus far described are transcriptionally inactive. We have found that the single copy of the IsTat 1.1 VSG gene in the IsTaR 1 serodeme has a telomeric location on a minichromosome when inactive. When it is activated, it is not duplicated and remains on a minichromosome. These data indicate that minichromosomes contain or can acquire all the DNA sequences necessary in cis for VSG gene expression and antigenic switching. Of several sequences associated with expressed VSG genes or their transcripts, only the 76-base pair (bp) repeat element was found in minichromosomal DNA. Variant antigenic types (VATs) which occurred immediately before and after VAT-1, expressed VSG genes located on larger chromosomes. Thus, different chromosomes can act as VSG gene expression sites.