The male reproductive system of the barnacle Semibalanus balanoides (Linnaeus, 1767) is a perfect model system for investigating naturally occurring cyclic nonpathological degeneration and programmed cell death (PCD). Every year after copulation, the barnacle degenerates its gonads, eggs, spermatids and penis initiated by severe environmental constraints. This is apparently a useful strategy for saving energy. By careful ultrastructural and immunohistochemical analysis of the male reproductive organs, we identiWed autophagic cell death in the penis and spermatids, both morphologically on ultrathin sections as well as histochemically for the Wrst time on semithin tissue sections with the new antibody against microtubule-associated protein 1 light chain 3 (LC3). Apoptosis in the testis and vesicula seminalis was determined based on the morphological characters on the apoptosis-speciWc antibody against the apoptosis inducing factor (AIF), and on positive TUNEL (terminal in situ nick end labeling) nuclei. Secondary necrosis in late degrading stages occurred in all tissues investigated, based on morphological characters and weak TUNEL staining. Moreover, the ultrastructural screening showed transient forms of cell death in the ductus ejaculatorius epithelium, the epidermis, and the longitudinal muscles of the penis. According to the immunohistochemical tests, the cyclic degeneration of the male reproductive system follows a sequence of programmed cell death modes from autophagic cell death via apoptosis to secondary necrosis.