Trypanosoma brucei (T. brucei) parasites cause two major infectious diseases in Africa: African trypanosomiasis in humans (HAT) and Nagana in animals. Despite the enormous economic and social impact, vaccines and reliable diagnostic measures are still lacking for these diseases. The main obstacle to developing accurate diagnostic methods and an active vaccine is the parasite’s ability for antigenic variation, impairment of B cell maturation, and loss of B cell memory which collectively prevent the development of a long-lasting, effective immune response. The antigenic variation is sustained by random gene switching, segmental gene conversion, and altered glycosylation states of solvent-exposed regions of the corresponding variant surface glycoproteins (VSGs). These glycoproteins use a glycosylphosphatidylinositol (GPI) anchor for attachment to the membrane. GPIs of T. brucei have specific branched structures that are further heterogeneously galactosylated. Here, we synthesized a glycan fragment library containing T. brucei GPIs’ most prominent structural features and performed an epitope mapping using mice and human sera of infected specimens using glycan microarrays. The studies indicate that in contrast to VSGs, T. brucei GPIs are recognized by infection-induced short-lived Immunoglobulin M (IgM) and long-lasting Immunoglobulin G (IgG), suggesting a specific immune response against GPI structures. These findings enable the development of diagnostic tests based on synthetic antigens for the reliable diagnosis of human African trypanosomiasis and Nagana.