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The diameter and compositional variations of magnetic crystal grains in a CoCrPt-SiOx perpendicular magnetic recording medium were investigated by using a transmission electron microscope equipped with an energy-dispersive X-ray spectrometer. The grain boundary composition was estimated from the average film and the average grain compositions by taking account of their volumes. It has been shown that the composition of individual grain depends little on grain diameter. The variations in the magnetic anisotropy energy and the saturation magnetization are estimated from the compositions of individual magnetic crystal grains. The thermal stability of magnetic crystal grain is discussed on the basis of the estimated K u V/kT value.