Apoptosis of enterocytes is a feature that characterises the development of lesions in coeliac disease (CD). However, the intracellular pathways that lead to apoptosis of enterocytes have not been completely clarified. Bak is a member of the Bcl-2 family of proteins that acts as an endogenous promoter of apoptosis in normal enterocytes. However, its role in coeliac lesions has not been explored. We used small intestinal mucosa from patients with CD to evaluate the differential expression of members of the Bcl-2 family of proteins. Gene expression of Bak was analysed by RT-PCR of biopsies from 14 patients with untreated CD and from 19 controls without CD. In these samples, we also investigated the localisation of the Bak protein by immunohistochemistry and its apoptotic activity. In patients with untreated CD there was a 2.3-fold higher expression of Bak mRNA (p = 0.026), without significant differences in the expression of related genes bax or bcl-2. The higher expression of interferon gamma (IFN-gamma) (p = 0.036) and the higher number of apoptotic cells identified by the TUNEL method (p = 0.032) confirmed the proapoptotic status in the intestinal mucosa of CD patients. We found a significant positive correlation (p < 0.0001) between the expression of IFN-gamma and Bak mRNA in patients with untreated CD. The expression of Bak protein was higher in patients with CD, and the immunoreactivity was almost restricted to the epithelium. We found that Bak mRNA and its protein were overexpressed in the intestinal lesions of CD patients and that IFNgamma confers increased susceptibility for enterocytes to undergo apoptosis via upregulation of Bak.