Distributions of fish otoliths and squid beaks in the stomach, small intestine, and large intestine of northern fur seal (Callorhinus ursinus) were examined to assess their relevance to biases in diet estimation by scat analysis. The contents of the digestive tracts of 51 seals collected in the western North Pacific off northern Japan were inspected. The large intestines contained more fish otoliths and squid beaks than either the stomachs or the small intestines. The prey composition estimated from hard parts in the small intestines was similar to the large intestines, but there was a greater dominance of squid in the stomachs. Squid beaks found in the digestive tracts ranged from 2.26-22.20 mm in wing length, although large beaks (≥10 mm) were found only in the stomachs. In addition, there were significant differences in the sizes of fish otoliths found in the stomachs and the large intestines. The difference of the prey composition and the size may have resulted from the limited passage of large particles at the pyloric end of the stomach. In order to improve the accuracy of scat analysis, we must investigate to restrict passing the large particles.