The hearts, diaphragms, hind legs, and back muscles of 64 Japanese sika deer (Cervus nippon centralis) caught in a mountainous area of Hyogo Prefecture, Japan, were examined for Sarcocystis infection by detecting sarcocysts. Sarcocysts were detected in the muscles of 52 (81.3%) individuals, and their prevalence did not differ among 1-5-year-old individuals, although no sarcocysts were detected in deer younger than 1 year old. Sarcocyst prevalence was significantly lower in the back muscles than in the other tissues. The intensity of sarcocyst infection was also significantly higher in the heart than in any other organ examined. This high prevalence of Sarcocystis infection in Japanese sika deer may be attributable to their frequent contact with the feces of the final hosts, including the hunting dogs that accompany hunters culling deer, and stray dogs, wild foxes, and raccoon dogs. The detected sarcocysts were oval to rod-like in shape and the internal section was divided by septa into many compartments. Many crescent-shaped bradyzoites were present in each compartment. The average size of 177 sarcocysts was 698.5×170.2μm. However, the measurements ranged widely, with lengths of 243.0-1,067.4μm and widths of 58.7-351.1μm. The variation of the sizes of the sarcocysts did not correlate with their shape or location of parasitization in the host.