Variant surface antigens have been purified from variants of a newly developed serodeme of Trypanosoma brucei 164, and found to be distinct by immunological and molecular criteria. cDNA clones containing variant and invariant gene sequences were isolated by using RNA from different variants and cloned DNAs from other systems as probes. These trypanosome and heterologous cloned DNAs were used as probes of trypanosome gene structure and activity. Regulation of variant antigen gene expression is at the level of transcription, and the variant antigen genomic sequences differ in their arrangement between the variants. Chick α- and β-tubulin sequences hybridize to trypanosome-tubulin gene sequences, while chick β-actin sequences do not. A 1650 bp β-tubulin trypanosome cDNA has been isolated. The trypanosome α- and β-tubulin sequences appear to be clustered in the genome. Sequence rearrangement of tubulin genes does not occur during antigenic variation.