Septoria tritici blotch caused by the fungus Zymoseptoria tritici is one of the most devastating foliar diseases of wheat. Knowledge regarding mechanisms involved in resistance against this disease is required to breed durable resistances. We compared here the expression of defense and pathogenicity determinants in three cultivars in semi-controlled culture conditions. The most susceptible cultivar, Alixan, presented higher necrosis and pycnidia density levels than Altigo, the most resistant one. In Premio, a moderately resistant cultivar, necrosis developed as in Alixan, while pycnidia developed as in Altigo. In non-infectious conditions, genes encoding for PR1 (pr1), glucanase (gluc) and allene oxide synthase (aos) were constitutively expressed at a higher level in both Altigo and Premio than in Alixan, while chitinase2 (chit2), phenylalanine ammonia lyase (pal), peroxidase (pox2) and oxalate oxidase (oxo), were expressed at a higher level in Premio only. Except for aos, all genes were induced in Alixan during the first steps of the infection symptomless phase. Only pox2, oxo, gluc and pal and pal, chs and lox genes were up-regulated at some time points in Altigo and Premio, respectively. Basal cultivar-dependent resistance against Z. tritici could therefore be explained by various genes expression patterns than high expression levels of given genes. During the necrotrophic phase, Z. tritici cell-wall degrading enzyme activity levels were lower in Altigo and Premio than in Alixan, and were associated more with pycnidia than with necrosis. Similar tissue colonization occurred in the three cultivars, suggesting an inhibition of the switch to the necrotrophic lifestyle in Altigo.