Since 1989, the Witches' broom disease due to the pathogenic fungus Crinipellis perniciosa increased in Bahia, Brazil, destroying the cultivation of cacao trees and leading to important economical and social changes in the concerned areas such as in the Bahia state. The aim of the research developed in the laboratory is to acquire a good knowledge of the determinism of the interaction between the cacao tree and the pathogen Crinipellis based on functional genomic and proteomic studies, and to contribute to the development of effective methods for the genetic improvement of resistance to this disease, so as to create new varieties obtained through a Marker-Assisted Selection (MAS) strategy. We report here studies related to gene expression in meristems of resistant and susceptible cacao trees inoculated or not with C. perniciosa spores. Plants were harvested from time zero up to 70 days after inoculation (necrosis symptoms), and used to generate Expressed Sequence Tags (ESTs). First, we developed a successful and reliable procedure for the isolation of RNA from any cacao tissues particularly those containing a high content of polyphenols and polysaccharides such as meristems and fruits. Then, we generated two cDNA libraries corresponding to inoculated resistant and susceptible plants, and we are randomly sequencing and analyzing using bioinformatics tools, 10 000 ESTs of both libraries. Interestingly, the sequences obtained from susceptible plants are closely related to genes involved in program cell death. The results obtained using the genomics tools developed in our laboratory provide new data about the physiology of the interaction between Theobroma cacao and Crinipellis perniciosa. In a short term we plan to do functional analyses of some candidate genes, which can be used for mapping, to facilitate introgression strategies and to create new varieties resistant to Crinipellis perniciosa. These data may also be related to research on gene expression of cacao chal