To identify the molecular mechanism which primarily plays a role in the pathogenesis of Crohn's disease (CD) without prior hypothesis, differential display method was employed to detect differentially expressed genes between the inflamed and uninflamed colonic samples from one patient with CD. The mRNA levels of these genes were subsequently semi-quantitated in affected and unaffected tissues from six patients using reverse transcriptase polymerase chain reaction (RT-PCR). Six genes including long form FLICE inhibitory protein (FLIPL) were found to be consistently overexpressed in the inflamed colonic CD tissues. Immunohistochemical studies revealed that FLIPL expressing cells were lamina propria lymphocytes (LPLs). The present study suggested that overexpression of FLIPL in the LPLs may be involved in the pathogenesis of CD through defective activation-induced cell death. In addition, this study provided evidence for a possible role of several previously unsuspected genes in the pathogenesis of CD.