A strategy was developed to isolate Nanobodies, camelid-derived single-domain antibody fragments, against the parasite infectome without a priori knowledge of the antigens nor having access to the purified antigens. From a dromedary, infected with T. evansi, we cloned a pool of Nanobodies and selected after phage display 16 different Nanobodies specific for a single antigen, i.e. variant surface glycoprotein of T. evansi. Moreover 14 Nanobodies were isolated by panning on different total parasite lysates. Thus, this anti-infectome experiment generated Nanobodies, monospecific for one Trypanosoma species, whereas others were pan-reactive to various Trypanosoma species. Several Nanobodies could label specifically the coat of a set of Trypanozoon species. The recognized target(s) are present in GPI-linked membrane fractions of bloodstream- and fly-form parasites. Due to the omnipresence of these targets on different parasite species and forms, these antibody fragments are a valuable source for validation of novel, not yet identified targets to design new diagnostics and therapeutics.