African trypanosomiasis is a severe parasitic disease affecting both man and livestock. It is crucial to expand our fundamental knowledge of the intimate interactions between trypanosomes and their vertebrate hosts in order to develop new and efficient control strategies. The mouse model of trypanosomiasis is the most popular for research purposes because of all the logistic advantages of using this species. Studies of any aspect of trypanosomiases in the mouse systematically require the quantification of some phenotypic traits which translate its degree of resistance/susceptibility to the disease, as blood cell counts. The present study presents a methodological approach combining everyday microsampling of tail blood and its analysis by flow cytometry. The technical options and conditions permitting a fast, reliable and reproducible daily quantification of erythrocyte, reticulocyte, leucocyte and trypanosome counts in the inoculated mouse were established. The protocol proposed allows the multiplication of blood samplings without being exposed to the time-consuming constraint of visual countings, without causing iatrogenic blood cell alterations in the mouse and without requiring specific anti-trypanosome antibodies.