Tsetse flies (Diptera: Glossinidae) are pupiparous insects that transmit African trypanosomes to humans and animals. Using three species of tsetse flies belonging to two subgenera, Nemorhina and Glossina, our data provide a first answer to the following question: do the juvenile stages of tsetse flies provide metric traits allowing reliable species and/or sex identification? We compared three species using their wings and their pupae: Glossina palpalis gambiensis, Glossina tachinoides and Glossina morsitans submorsitans. To separate size and shape information, 11 landmarks per wing were submitted to the Generalised Procrustes Analysis (GPA). The contour of the pupae was processed by elliptic Fourier analysis (EFA).A validated reclassification method was used to compare the taxonomic power of each organ, as well as its utility for sex recognition. The contour of the pupae did not provide a satisfactory species signal (75 %), relative to the one obtained from wing landmarks (99 %). However, the overall pupae size was much more satisfactory than the wings size (93 % versus 57 %). In spite of a lower taxonomic signal, the morphometric variation observed on pupae was in agreement with known phylogenetic relationships. Contrary to the wings, sexual dimorphism was much reduced in pupae and not strong enough to allow any reliable sex identification.