Although apoptosis has been implicated in the neuronal loss observed in prion diseases, the participation of apoptosis-related factors, like the Bcl-2 family of proteins, is still not clear. Moreover, there are conflicting data concerning the major role of apoptosis in the neuropathology associated with transmissible spongiform encephalopathies. Many studies have been developed in vitro or in experimentally infected animal models but, at present, little is known about this process in natural spontaneous and acquired prion diseases. In this work, the implication of Bax and Bcl-2 has been investigated by the analysis of their expression and protein distribution in medulla oblongata of naturally scrapie-infected sheep. Moreover, their spatial relationship with PrP(Sc) deposition, neuronal vacuolation and neuropil spongiosis has also been analysed as well as the possible induction of neuronal apoptosis in this model. Real Time RT-PCR showed overexpression of the pro-apoptotic gene Bax in scrapie medullas, and immunohistochemistry confirmed its accumulation. No variation of Bcl-2 was observed at the level of gene expression or protein production. Bax distribution, PrP(Sc) deposition, neuronal vacuolation and spongiosis were quantified in different medulla oblongata nuclei and their spatial relationship was evaluated. Bax staining showed a positive correlation with prion deposition, suggesting that this factor is involved in prion neurotoxicity in our natural model. Despite Bax overexpression, neuronal apoptosis was revealed neither by TUNEL nor by immunohistochemical detection of the activated form of caspase-3. This lack of apoptosis could be attributed to the relatively low number of neurons in this area or to the existence of neuroprotective mechanisms in medulla oblongata motor neurons.