African trypanosomes are vector-borne haemoparasites that cause animal and human African trypanosomiasis. Survival in the mammal host is mediated by antigenic variation, an immune evasion mechanism based on the sequential replacement of the Variant Surface Glycoprotein (VSG) coat that covers the parasite surface. As the main factors in the host-trypanosome interaction, VSG expression and structure has been extensively studied in Trypanosoma brucei. Since trypanosome genomes contain hundreds of highly dynamic VSG genes, studies of VSG diversity are challenging and have been limited to reference strains. However, we expect VSG diversity to be vitally important to disease, both during individual infections and across parasite populations. This thesis examines VSG sequence diversity within and between trypanosome populations to produce new approaches to measuring VSG diversity and a holistic view of antigenic diversity in trypanosome genomes. In chapters two and five, I present ���variant antigen profiling��� as a method to characterise VSG repertoires in genomic and transcriptomic data from T. congolense and T. vivax respectively. Due to species differences in VSG repertoire composition, bespoke methodologies were required. Analysing VSG diversity over space and time was a challenge to conventional techniques that can now be overcome. In chapter three, I apply variant antigen profiling to metacyclic transcriptomes to characterise T. congolense metacyclic VSG expression in the tsetse fly. This revealed that specific phylotypes might be preferentially expressed in infective, metacyclic-stage parasites, which can be taken forward in field experiments. In chapter four I present a description of putative T. congolense expression sites, which are compared to T. brucei. In chapter six, I present a comparative analysis of the balance of evolutionary forces affecting molecular evolution of VSGs in T. brucei, T. congolense, and T. vivax. These two chapters bring new insights into antigenic variation evolution in African trypanosomes, aiding the reconstruction of the process of host-parasite coevolution. Collectively, this work makes a substantial, original contribution to our understanding of antigenic diversity in African trypanosomes, whilst revealing the need for revisiting basic questions of the mechanisms of antigenic variation in T. congolense and T. vivax. Such projects will certainly be aided by the multiple applications of variant antigen profiling to gene expression, functional and population studies.