We applied the grazing exit electron probe microanalysis (GE-EPMA) to analyses of a submicrometer precipitate, which consisted of Si and Ni, in a copper base alloy. We measured X-rays emitted from the precipitate projected onto the etched sample surface with a conventional EPMA method (exit angle: 30°) and grazing exit conditions (exit angle: near 0°). We also measured X-rays emitted from precipitates extracted from the matrix by the EPMA method and compared the results. Characteristic X-rays of Cu emitted from the interior of the matrix as well as the background X-rays drastically decreased in the GE-EPMA spectrum, as compared to that of the conventional EPMA method. We, then, could observe the X-ray peaks of Si and Ni emitted solely from the analyzed precipitate with extremely low background in the GE-EPMA spectrum. The Si Kα/Ni Kα net intensity ratio in the GE-EPMA spectrum was, however, much different from that of the conventional EPMA method or those of the extracted precipitates. These results indicated that the X-ray intensities in the GE-EPMA analysis were affected by the X-ray absorption by other precipitate projected onto the surface or projection parts of the matrix in extremely low exit angles.