Legume plants play an important role in ecology and agronomy due to their symbiotic interactions with nitrogen-fixing bacteria. They provide protein-rich food to animals and humans in the absence of nitrogen fertilizers, contributing thus to a sustainable agriculture. However, their culture may suffer high yield losses due to diseases and pests. Among the foliar fungal diseases, Ascochyta blight is one of the most severe and affects many legume crops worldwide. In our work, we established that the pathogen of Pea, Ascochyta pisi, is also a pathogen of the model plant Medicago truncatula, and we took advantage of this pathosystem to identify genes putatively involved in tolerance or susceptibility to the disease by an improved derivate of Serial Analysis of Gene Expression. The quantitative gene expression profile of two differentially susceptible lines (mock-inoculated and inoculated with A. pisi) was assessed by SuperSAGE on pooled material of a time-course experiment. The 4 libraries generated more than 16 Mio sequenced 26 bp-Tags. Statistical analysis of the 38018 unique sequences (uniTags) identified 2343 annotated genes and revealed a significant differential expression for 1696 among them. BLAST2Go annotation showed that a majority (>75%) of the sequences belonged to the classes metabolic process, cellular process, response to stimulus and biological regulation. The two M. truncatula lines were susceptible, but differed in the speed of disease development. Gene expression profiles of these two lines in response to A. pisi showed quantitative and qualitative differences.