African trypanosomiases are parasitic diseases transmitted by tse-tse flies, considered as the main sanitary obstacle to animal production development in sub-Saharan Africa. However, if trypanosomiases have dramatic consequences on zebu (Bos indicus) populations, they have a weaker impact on the western African taurine (Bos taurus), which is known to be naturally tolerant to trypanosome infection. Mechanisms governing this trypanotolerant trait are still poorly understood, but today, recent postgenomic biotechnologies, such as the SAGE technique (serial analysis of gene expression) allow us to explore the full transcriptome. Twelve SAGE libraries were constructed from two trypanotolerant animals (N'Dama and Baoulé) and one susceptible species of cattle (the Sudanese zebu) during an experimental Trypanosoma congolense infection; 43,458 different tags were obtained at several particular points during the infection (before infection, at the maximum of parasitemia, the maximum of anemia, and at the end of the experiment after value normalization). Bioinformatics analyses highlighted some interesting gene variations with respect to the trypanotolerance status of the animal.