The flank organ of the Syrian hamster shows a biodynamic response to androgenic stimulation and is, therefore, a suitable model for the study of androgenic effects on hair and sebaceous glands. This organ is susceptible to programmed cell death (PCD), a prominent feature associated with sexual organ adjustment. In the present report, the type of PCD (apoptosis or autophagy) exhibited by this organ was evaluated. Caspase-3 activity, indicative of apoptosis, was not detectable in flank organ homogenates. Furthermore, cytokeratins, which are normally degraded during apoptosis, remained intact. On the other hand, Western blotting of Beclin 1 and light chain 3-II, both important autophagy markers, revealed autophagic processes in the flank organ in both sexes, especially in females. Cathepsin D activity, higher in males than in females, and procathepsin D expression were also consistent with autophagy and not apoptosis. Taken together, these data indicate that macroautophagy, and not apoptosis, is the main mechanism by which the flank organ responds to androgen. This is the first direct evidence establishing the relationship between autophagy and morphological changes in androgen-dependent organs.