Mice are still the most used model organism in initial phases of vaccine design. Bioinformatics is becoming increasingly more important in vaccine development, both for the design of novel simplified epitope-based vaccines and also in order to understand the specific immune response of selected vaccine formulations. Toxoplasma gondii, an intracellular parasite, causes severe neurologic and ocular disease in congenitally infected and immunocompromised individuals. No protective vaccine exists against human toxoplasmosis. However, studies with mice have revealed immunodominant cytotoxic T lymphocyte epitopes originating from type II strains. These verified epitopes might be useful in human vaccines as the peptide binding repertoire of H-2L(d) MHC and MHCs belonging to the HLA-B07 supertype are very similar. Here, the results obtained using these epitopes in BALB/c as well as transgenic HLA-B*0702 mice are discussed. The stunning results obtained from the use of refined computational methods for the prediction of cytotoxic T lymphocyte epitopes are also discussed. The results highlight some important issues regarding both the use of mice but also the choice of bioinformatics methods in vaccine development.