High resolution two-dimensional polyacrylamide gel (2D gel) electrophoresis and autoradiography were used to analyze the protein gene products of African trypanosomes biosynthetically labelled with [35S]methionine. Using cloned populations of parasites it was found that: antigenically different bloodstream trypanosomes from the same serodeme differed only in their variant surface glycoproteins; Trypanosoma brucei, T.b. rhodesiense and T.b. gambiense subspecies could be distinguished on the basis of differences in expressed proteins; transformation from bloodstream trypomastigotes to procyclic epimastigote culture forms was accompanied by loss of variant surface glycoproteins and several other qualitative and quantitative changes in minor proteins. The results indicate that 2D gel analysis may allow improved classification of African trypanosomes (based on the observation of hundreds of protein markers) and may also provide a general technique for the identification of lifecycle stage specific markers.