Leishmania parasites are able to interfere with host immune responses on many levels, as T cell responses balance, as observed in the murine model of infection. In the present study, we analyzed genes expression in both host and parasite during the progression of infection. Host genes associated to T-lymphocytes responses, MHC classes I and II, as well as parasite enzymes genes, cysteine-proteinases (CP) B and C, were examined in mice along evolution of infection by Leishmania (Leishmania) amazonensis. Murine strains with distinct levels of susceptibility to infection presented different patterns of MHC genes expression: MHC class I genes tend to have higher expression levels in CBA mice, whereas MHC class II genes expression predominates in BALB/c mice. CPB genes expression in the parasites was shown to predominate over CPC in both mice strains tested. Understanding genes expression patterns during infection may lead to new and more efficient treatments for leishmaniasis.