the objective of this work was to determine the transcript profile of tomato plants (lycopersicon esculentum mill.), during fusarium oxysporum f. sp. lycopersici infection and after foliar application of salicylic acid. the suppression subtractive hybridization (ssh) technique was used to generate a cdna library enriched for transcripts differentially expressed. a total of 307 clones was identified in two subtractive libraries, which allowed the isolation of several defense-related genes that play roles in different mechanisms of plant resistance to phytopathogens. genes with unknown roles were also isolated from the two libraries, which indicates the possibility of identifying new genes not yet reported in studies of stress/defense response. the ssh technique is effective for identification of resistance genes activated by salicylic acid and f. oxysporum f. sp. lycopersici infection. not only the application of this technique enables a cost effective isolation of differentially expressed sequences, but also it allows the identification of novel sequences in tomato from a relative small number of sequences.