Amyloidosis is a disease characterized by the tissue deposition of autologous extracellular fibrillar proteins that can result in compression of adjacent tissues. Amyloidosis is well-recognized in a wide variety of animals, including mammals, birds, and reptiles. However, to date, there is only one report of amyloidosis in cetaceans. During 1999 and 2000, among 12 Stejneger's beaked whales (Mesoplodon stejnegeri) that were stranded along the Sea of Japan's coast, amyloidosis was found in two whales (case 1, 498 cm, male; case 2, 520 cm, female). For this study population, the prevalence rate of amyloidosis was approximately 17%. These two animals were considered physically and sexually mature based on body length, external features, gonad characteristics, and skeletal features. Livers were notably swollen, fragile, and pale (brownish yellow) on gross examination. A large deposit of amyloid was found in Disse's spaces along with marked atrophy of the hepatocytes. Numerous granulomas, including many nematodes (Crassicauda sp.), were found along with amyloid deposition in the kidneys. Amyloid was also detected in the heart, spleen, adrenal gland, and pancreas. Amyloid in both cases was identified by typical morphology on H&E and Congo red staining. Electron microscopy displayed a typical network of fine fibrils measuring about 11 nm in diameter. This is the first report of amyloidosis in two Stejneger's beaked whales stranded on the coast of the Sea of Japan.